Peptide library obtained from multi-clade chimeric immunogens derived from highly conserved regions of the human immunodeficiency virus type 1 (HIV-1) consensus proteome

ABSTRACT

The present invention provides artificial fusion proteins (AFPs) designed to elicit an anti-HIV immune response, as well as nucleic acid molecules and expression vectors encoding those proteins. The AFPs of the invention may comprise domains from various HIV proteins, such as Gag, Pol, Vif, and Env proteins, which are partial sequences. HIVCON is an AFP in which the HIV domains are from several HIV Glade consensus sequences and which optionally contains additional domains which may be useful, for example, in monitoring expression levels or laboratory animal immune responses. Other aspects of the invention may include compositions and methods for inducing an anti-HIV immune response in a subject, preferably with a DNA prime-MVA boost strategy, and to induce a cell-mediated immune response.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.11/844,301 filed Aug. 23, 2007 now U.S. Pat. No. 7,981,430 issued Jul.19, 2011, which is a continuation-in-part application of internationalpatent application Serial No. PCT/IB2006/001909 filed 23 Feb. 2006,which published as PCT Publication No. 2006/123256 on 23 Nov. 2006,which claims benefit of U.S. provisional patent application Ser. No.60/655,764 filed 24 Feb. 2005.

The foregoing application, and all documents cited therein (“applicationcited documents”) and all documents cited or referenced in theapplication cited documents, and all documents cited or referencedherein (“herein cited documents”), and all documents cited or referencedin herein cited documents, together with any manufacturer'sinstructions, descriptions, product specifications, and product sheetsfor any products mentioned herein or in any document incorporated byreference herein, are hereby incorporated herein by reference, and maybe employed in the practice of the invention.

This work was funded, in part, by a grant from the Medical ResearchCouncil of the United Kingdom.

FIELD OF THE INVENTION

This invention relates to artificial fusion proteins (AFPs) designed toelicit an anti-HIV immune response in a subject, as well as nucleic acidmolecules and expression vectors encoding those proteins. The AFPs, aswell as nucleic acids and expression vectors encoding these proteins,may be administered alone or in combination to a subject to generate ananti-HIV immune response. The AFPs of the invention may comprise domainsfrom various HIV proteins, for example, Gag, Pol, Env, and Vif proteins.The HIV proteins that form the domains are partial protein sequences andbiologically inactivated for one or more of the normal activities ofthose proteins. HIVCON is an AFP in which the HIV domains are frommultiple HIV clads consensus sequences. HIVCON may also containadditional domains useful, for example, in monitoring protein expressionlevels or laboratory animal immune responses. Such domains areoptionally included in the AFPs. Other aspects of the invention includecompositions and methods for inducing an anti-HIV immune response in asubject, preferably using a DNA prime-MVA boost strategy and preferablyto induce a cell-mediated immune response.

BACKGROUND OF THE INVENTION

AIDS, or acquired immunodeficiency syndrome, is caused by humanimmunodeficiency virus (HIV) and is characterized by several clinicalfeatures including wasting syndromes, central nervous systemdegeneration and profound immunosuppression that results inopportunistic infections and malignancies. HIV is a member of thelentivirus family of animal retroviruses, which include the visna virusof sheep and the bovine, feline, and simian immunodeficiency viruses(SIV). Two closely related types of HIV, designated HIV-1 and HIV-2,have been identified thus far, of which HIV-1 is by far the most commoncause of AIDS. However, HIV-2, which differs in genomic structure andantigenicity, causes a similar clinical syndrome.

An infectious HIV particle consists of two identical strands of RNA,each approximately 9.2 kb long, packaged within a core of viralproteins. This core structure is surrounded by a phospholipid bilayerenvelope derived from the host cell membrane that also includesvirally-encoded membrane proteins (Abbas et al., Cellular and MolecularImmunology, 4th edition, W.B. Saunders Company, 2000, p. 454). The HIVgenome has the characteristic 5′-LTR-Gag-Pol-Env-LTR-3′ organization ofthe retrovirus family. Long terminal repeats (LTRs) at each end of theviral genome serve as binding sites for transcriptional regulatoryproteins from the host and regulate viral integration into the hostgenome, viral gene expression, and viral replication.

The HIV genome encodes several structural regulatory proteins. The Gaggene encodes core structural proteins of the nucleocapsid core andmatrix. The Pol gene encodes reverse transcriptase, integrase, and viralprotease enzymes required for viral replication. The tat gene encodes aprotein that is required for elongation of viral transcripts. The revgene encodes a protein that promotes the nuclear export of incompletelyspliced or unspliced viral RNAs. The Vif gene product enhances theinfectivity of viral particles. The vpr gene product promotes thenuclear import of viral DNA and regulates G2 cell cycle arrest. The vpuand nef genes encode proteins that down regulate host cell CD4expression and enhance release of virus from infected cells. The Envgene encodes the viral envelope glycoprotein that is translated as a160-kilodalton (kDa) precursor (gp160) and cleaved by a cellularprotease to yield the external 120-kDa envelope glycoprotein (gp120) andthe transmembrane 41-kDa envelope glycoprotein (gp41), which arerequired for the infection of cells (Abbas, pp. 454-456).

HIV infection initiates with gp120 on the viral particle binding to theCD4 and chemokine receptor molecules (e.g., CXCR4, CCR5) on the cellmembrane of target cells such as CD4+ T-cells, macrophages and dendriticcells. The bound virus fuses with the target cell and reversetranscribes the RNA genome. The resulting viral DNA integrates into thecellular genome, where it directs the production of new viral RNA, andthereby viral proteins and new virions. These virions bud from theinfected cell membrane and establish productive infections in othercells. This process also kills the originally infected cell. HIV canalso kill cells indirectly because the CD4 receptor on uninfectedT-cells has a strong affinity for gp120 expressed on the surface ofinfected cells. In this case, the uninfected cells bind, via the CD4receptor-gp120 interaction, to infected cells and fuse to form asyncytium, which cannot survive. Destruction of CD4+T-lymphocytes, whichare critical to immune defense, is a major cause of the progressiveimmune dysfunction that is the hallmark of AIDS disease progression. Theloss of CD4+ T cells seriously impairs the body's ability to fight mostinvaders, but it has a particularly severe impact on the defensesagainst viruses, fungi, parasites and certain bacteria, includingmycobacteria.

The different isolates of HIV-1 have been classified into three groups:M (main), O (outlier) and N (non-M, non-O). The HIV-1 M group dominatesthe global HIV pandemic (Gaschen et al., (2002) Science 296: 2354-2360).Since the HIV-1 M group began its expansion in humans roughly 70 yearsago (Korber et al., Retroviral Immunology, Pantaleo et al., eds., HumanaPress, Totowa, N.J., 2001, pp. 1-31), it has diversified rapidly (Junget al., (2002) Nature 418: 144). The HIV-1 M group consists of a numberof different clades (also known as subtypes) as well as variantsresulting from the combination of two or more clades, known ascirculating recombinant forms (CRFs). Subtypes are defined as havinggenomes that are at least 25% unique (AIDS epidemic update, December2002). Eleven clades have been identified and a letter designates eachsubtype. When clades combine with each other and are successfullyestablished in the environment, as can occur when an individual isinfected with two different HIV subtypes, the resulting virus is knownas a CRF. Thus far, roughly 13 CRFs have been identified. HIV-1 cladesalso exhibit geographical preference. For example, Clade A, thesecond-most prevalent Glade, is prevalent in West Africa, while Clade Bis common in Europe, the Americas and Australia. Clade C, the mostcommon subtype, is widespread in southern Africa, India and Ethiopia(AIDS epidemic update, December 2002).

This genetic variability of HTV creates a scientific challenge tovaccine development. HIV-1 is a highly variable virus, for whichintra-subtype variation can be as high as 20% and inter-subtypedifferences can reach 35% of the amino acid sequence (Thomson, M. M. etal (2002) Lancet Infect Dis. 2: 461-471). Although some reports havedemonstrated that cross-clade immune responses can be detected (Cao, H.et al. (1997) J. Virol. 71: 8615-8623; Ferrari, G. et al. (1997) Blood90: 2406-2416; Walker, B. D. et al. (2001) Nat. Immunol. 2: 473-475),other studies conflict (Burrows, S. R. et al. (1992) Eur. J. Immunol.22: 191-195; McMichael, A. J. et al (2002) Nat. Rev. Immunol. 2:283-291). Thus, unless clear evidence for very broad cross-cladereactivity becomes available and it is shown that vaccines can inducestrong T-cell responses to many epitopes, it is prudent to match thevaccine immunogens to the Clades and/or CRFs in the target population.

Traditional approaches to vaccine development, such as immunization withlive attenuated virus, killed virus or viral subunits, are not provingfeasible for HIV. For example, in the macaque-SIV model, live attenuatedvaccines cause persistent infection, with some macaques developing AIDS.Moreover, it has been difficult to generate effective neutralizingantibodies to clinical isolates of virus. Combinations of traditionaland new approaches with novel immunogens designed to elicit humoraland/or cellular immunity may prove necessary and are being activelysought.

With the difficulties encountered for neutralizing antibodies, anotherapproach to HIV vaccine development is to induce cell-mediated immuneresponses. Such responses are predominantly mediated by cytotoxic Tlymphocytes (CTLs). CTLs, also known as CD8+ T-cells, participate in anorganism's defense in at least two different ways: by killingvirus-infected cells and by secreting a variety of cytokines andchemokines that directly or indirectly contribute to the suppression ofvirus replication. The induction and maintenance of strong CD8+ T cellresponses require “help” provided by CD4+ T-lymphocytes (helperT-cells).

CTLs recognize peptides that originate from both surface and innerstructural and nonstructural HIV proteins. Unlike antibodies, theycannot prevent cell-free HIV from infecting host cells. Therefore, thevaccine-induced prophylactic CTLs must act quickly. For that, they mayhave to be in sufficient numbers, which may or may not requirepersistent vaccine stimulation or regular re-vaccinations. Preferably,vaccine-induced CTLs should recognize early and/or abundant HIV proteinsof the transmitting virus/clade, target multiple CTL epitopes infunctionally conserved protein regions to make it difficult for HIV toescape, and kill target cells efficiently.

To induce CTLs, a prime-boost immunization strategy using plasmid DNAencoding an immunogen as a priming immunization, followed by a boostingimmunization with a recombinant virus encoding the same immunogen, hasdemonstrated efficacy to stimulate CD8+ T cell responses in mice (Hankeet al., (1998a) Vaccine 16:439-445; Schneider et al., (1998) Nat. Med.4:397-402; Kent et al., (1998) J. Virol. 72:10180-10188). This strategyhas been confirmed and extended for non-human primates (Hanke et al,(1999) J. Virol 73:7524-7532; Allen et al., (2000a) J. Immunol. 164:4968-4978; Amara et al., (2001) Science 292:69-74; Allen et al., (2002)J. Virol. 76:10507-10511; Shiver et al., (2002) Nature 415:331-335) andhumans (McConkey et al., (2003) Nat. Med. 9:729-35). WO 98/56919discloses a prime-boost immunization strategy to generate a CTL-mediatedimmune response against malarial and other antigens, such as viral andtumor antigens. This immunization strategy uses priming and boostingcompositions, which deliver the same CTL epitope in different vectors,where the vector for the boosting composition is a replication-defectivepoxvirus vector.

Another aspect of vaccine development is to find formulations capable ofinducing CTL responses specific for multiple HIV epitopes. Such vaccinescould make it relatively difficult for HIV to escape and would have abetter chance to suppress HIV replication. Theoretically, severalsmaller immunogens delivered individually by separate vaccine vectorswould be advantageous over one large multigenic protein expressed from asingle vector, because the former immunogens may reach separateantigen-presenting cells and each induce at least one immunodominantresponse (Singh, R. A. et al., (2002) J. Immunol. 168:379-391). With amultigenic protein, unless cross-priming plays a role in immunestimulation, each component is produced by one cell and thus competeswith the others for presentation. Hence, a balance is needed between thebreadth of elicited immune responses and practicalities of vaccinedevelopment and production, the former increasing and the latterdecreasing the number of vaccine components.

Yet another aspect of vaccine development is to address HIV variability.First, vaccines could alternate HIV Clades using one protein from eachClade in their formulations. Second, a cocktail of all immunogensderived from the two or three most common HIV Clades could be used,because the immune system has the capacity to respond to many differentepitopes. However, as for other vaccine approaches, “immunodominance” ofepitopes could narrow the breadth of T cell responses and preventprophylactic immunity in response to viral infection (Yewdell, J. W. etal. (1999) Ann. Rev. Immunol. 17: 51-88).

During the course of a viral infection, CTL responses develop apredictable bias in their pattern of epitope recognition. A hierarchy ofepitope recognition develops, with most of the CTL response targeted toa very limited number of epitopes. This phenomenon is also known as“immunodominance”. Experimental evidence suggests that immunodominancedevelops as a consequence of many factors, such as the variety ofepitope affinities for the relevant cellular receptor, i.e., majorhistocompatibility complex (MHC) Class I molecule, the various copynumbers of the epitopes produced by the virus, and differences inepitope processing by the host cellular machinery. Therefore, vaccinestrategies that can bypass the hierarchy of epitope bias could result ina broad CTL response that provides a protective immune response againstviral infection.

With a few exceptions, most of the known CTL epitopes have beenidentified in chronically infected individuals and responses to theseepitopes have heretofore failed to protect against HIV infection.However, other studies have illustrated that the dominant response isnot necessarily the most protective (Gallimore, A. et al (1998) J. Exp.Med. 187: 1647-1657). It is therefore a highly desirable advance in theart to develop HIV immunogens based on conserved protein regions, whichare, by definition, common to all Clades (Wilson, C. C. et al. (2003) J.Immunol. 171: 5611-5623). Such an immunogen could comprise conservedprotein regions that do not necessarily contain epitopes that arenaturally processed by HIV-infected cells, but also comprise subdominantor cryptic epitopes that may be protective. An immunogen capable ofinducing strong responses against subdominant epitopes could avoid theproblem of immunodominance and therefore, induce broad T-cell responses.Further, cross-Glade or Glade-universal CTL reactivity could allow forless localized geographic use of such an immunogen.

Citation or identification of any document in this application is not anadmission that such document is available as prior art to the presentapplication.

SUMMARY OF THE INVENTION

It has now been surprisingly discovered that the sequences selected fromthe most highly conserved regions of selected HIV proteins, such as Gag,Pol, Vif, and Env, can induce immune responses against HIV that are notrestricted by HIV Clade or CRF. The present invention therefore, incertain embodiments, provides an artificial fusion protein (hereinafter“AFP”) comprising HIV sequences from Gag, Pol, Vif, and Env, wherein thesequences may comprise the most highly conserved regions of Gag, Pol,Vif, and Env, and which are selected irrespective of Clade, CRF, or thepresence or abundance of dominant CTL epitopes. Also provided areisolated nucleic acids expressing the AFP, expression vectors and hostcells which may comprise the nucleic acid expressing the AFP, methodsfor expressing the AFP, and methods for inducing immune responses to theAFP in a subject.

Accordingly, one aspect of the present invention provides an AFP whichmay comprise an HIV Gag domain, one or more HIV Pol domains, an HIV Vifdomain, and one or more HIV Env domains. In one embodiment, each of theHIV Gag, Pol, Vif, and Env may be selected so that the AFP induces animmune response to a pre-determined HIV Clade. In an alternativeembodiment, the amino acid sequences for each of the HIV Gag, Pol, Vif,and Env domains may be selected from HIV consensus sequences fordifferent HIV Clades. Preferably, the HIV Clade may be selected from thegroup consisting of Clade A, A1, A2, B, C, and D.

Another embodiment relates to the amino acid sequences for each of HIVGag, Pol, Vif, and Env, which may vary by from about 0% to about 10%between HIV Clades. Preferably, the sequences may vary from about 0% toabout 8% between Clades, and even more preferably, from about 0% toabout 6% between Clades.

In another embodiment, the domains may be present from N- to C-terminusin any order that does not recreate a naturally-occurring protein.Preferably, the domains may be present from N- to C-terminus in orderof: HIV Gag domain, a first HIV Pol domain, HIV Vif domain, a second HTVPol domain, a first HTV Env domain, a third HIV Pol domain, and a secondHIV Env domain. The domains may be joined with or without interveningsequences.

The HIV Gag domains preferably may comprise a sequence of amino acidsfrom an HIV isolate or an HIV consensus sequence corresponding to aminoacids 1-135 of SEQ ID NO: 2. The HIV Gag domain may comprise three HIVGag subdomains, which can be from the same HIV Clade, or from differentHIV Clades. In a preferred embodiment, the first HIV Gag subdomain maycomprise amino acids 1-56 of SEQ ID NO: 2 and the sequence is from HIVClade C. The second HIV Gag subdomain preferably comprises amino acids57-96 of SEQ ID NO: 2 and the sequence may be from HTV Clade D. Thethird HIV Gag subdomain preferably may comprise amino acids 97-135 ofSEQ ID NO: 2 and the sequence may be from HIV Clade A.

The HIV Pol domains preferably may comprise three HIV Pol domains,wherein the first HIV Pol domain preferably may comprise amino acids136-393 of SEQ ID NO: 2, the second HIV Pol domain preferably maycomprise amino acids 422-484 of SEQ ID NO: 2, and the third HIV Poldomain preferably may comprise amino acids 522-723 of SEQ ID NO: 2.Preferably, each HIV Pol domain may comprise at least two HIV Polsubdomains. The at least two HIV Pol subdomains may be from the same ordifferent HIV Clades. The first HIV Pol subdomain of the first HIV Poldomain preferably may comprise amino acids 136-265 of SEQ ID NO: 2 andthe sequence may be from HIV Clade B. The second HIV Pol subdomain ofthe first HIV Pol domain preferably may comprise amino acids 266-393 ofSEQ ID NO: 2 and the sequence may be from HIV Clade C. The first HIV Polsubdomain of the second HIV Pol domain preferably may comprise aminoacids 432-467 of SEQ ID NO: 2 and the sequence may be from HIV Clade A.The second HIV Pol subdomain of the second HIV Pol domain preferably maycomprise amino acids 468-494 of SEQ ID NO: 2 and the sequence may befrom HIV Clade B. The first HIV Pol subdomain of the third HIV Poldomain preferably may comprise amino acids 522-556 of SEQ ID NO: 2 andthe sequence may be from HIV Clade D. The second HIV Pol subdomain ofthe third HIV Pol domain preferably may comprise amino acids 557-629 ofSEQ ID NO: 2 and the sequence may be from HIV Clade A. The third HIV Polsubdomain of the third HIV Pol domain preferably comprises amino acids630-676 of SEQ ID NO: 2 and the sequence may be from HIV Clade B. Thefourth HIV Pol subdomain of the third HIV Pol domain preferably maycomprise amino acids 677-723 of SEQ ID NO: 2 and the sequence may befrom HIV Clade C.

The HIV Vif domain preferably may comprise amino acids 394-421 of SEQ IDNO: 2 and the sequence may be from HIV Clade D. The first HIV Env domainpreferably may comprise amino acids 485-521 of SEQ ID NO: 2 and thesecond HIV Env domain preferably may comprise amino acids 724-777 of SEQID NO: 2. The first HIV Env domain may be preferably from HIV Clade C,and the second HIV Env domain may be preferably from HIV Clade D. Thepresent invention also provides an AFP comprising amino acids 1-777 ofSEQ ID NO: 2. The AFPs of the present invention may also furthercomprise one or more non-human CTL domains for monitoring immuneresponses to the AFP in a laboratory animal, such as those selected fromthe group consisting of the SIV tat CTL epitope, the pb9 epitope, theP18-I10 epitope, and the SIV gag p27 epitope. The AFPs of the presentinvention may also further comprise a marker domain selected from thegroup consisting of Pk, Flag, HA, myc, GST or His epitopes. A furtheraspect of the invention provides an AFP comprising amino acids 1-806 ofSEQ ID NO: 2.

Another aspect of the present invention provides isolated nucleic acidswhich may have a nucleotide sequence encoding the AFPs of the invention.Further, the invention also provides expression vectors comprising anucleic acid having a nucleotide sequence encoding the AFP of thepresent invention, operably linked to at least one nucleic acid controlsequence. The nucleic acids and vectors of the invention areparticularly useful for providing genetic vaccines, i.e. vaccines fordelivering the nucleic acids encoding the AFPs of the present inventionto a subject such as a human, such that the AFPS are then expressed inthe subject to elicit an immune response.

The expression vector may be a plasmid vector, a viral vector, an insectvector, a yeast vector, or a bacterial vector. Preferably, the plasmidvector is pTH or pTHr.

The viral vector may be an alphavirus replicon vector, anadeno-associated virus vector, an adenovirus vector, a retrovirusvector, a poxvirus vector, or any other suitable viral vector. When thevector is a poxvirus vector, the poxvirus vector is selected from thegroup consisting of vaccinia virus and avipox virus. The poxvirus may bean attenuated poxvirus, such as MVA, NYVAC, TROVAC, or ALVAC.

The expression vector may also be a bacterial vector, such as a liveattenuated Salmonella or a Shigella vector.

In preferred embodiments, the nucleic acid control sequence may be acytomegalovirus (CMV) immediate early promoter.

Preferably, the codons encoding the AFPs of the invention may be thoseof highly expressed genes for a target subject or host cell in which theAFP is to be expressed. The subject is advantageously a human. Incertain embodiments, the expression vector pTH or pTHr may contain theHIVCON coding sequence and is referred to as pTH.HIVCON or pTHr.HIVCON,respectively. Alternatively, the expression vector MVA may be usedresulting in and nucleic acid referred to as MVA.HIVCON.

A further aspect of the present invention provides host cells comprisingthe expression vectors of the invention.

The invention also provides a method of preparing an AFP, which maycomprise (a) culturing the host cell of the invention for a time andunder conditions to express the AFP; and (b) recovering the AFP.

Another aspect provides methods for introducing into and expressing anAFP in an animal, which may comprise delivering an expression vector ofthe invention into the animal and thereby obtaining expression of theAFP in the animal.

Methods for expressing an AFP in animal cells are also provided, whichmay comprise (a) introducing an expression vector of the presentinvention into the animal cells; and (b) culturing those cells underconditions sufficient to express the AFP.

A further aspect of the present invention provides methods for inducingan immune response in an animal, which may comprise delivering anexpression vector of the invention into the animal, wherein the AFP isexpressed at a level sufficient to induce an immune response to the AFP.

Methods of inducing an immune response against HIV in a human subjectare also provided, which may comprise administering an immunogen one ormore times to a subject, wherein the immunogen is selected from thegroup consisting of (i) an AFP of the invention, (ii) a nucleic acidencoding the AFP, and (iii) an expression vector encoding the AFP; andwherein the AFP is administered in an amount or expressed at a levelsufficient to induce an HIV-specific CTL immune response in the subject.Preferably, the subject receives at least two administrations of theimmunogen, or a vector or nucleic acid encoding the immunogen, atintervals of at least two weeks or at least four weeks. Anotherembodiment provides another HIV immunogen administered at the same timeor at different times as part of an overall immunization regime.

Yet another aspect of the present invention provides methods of inducingan immune response against HIV in a human subject, which may compriseadministering to the subject at least one priming dose of an HIVimmunogen and at least one boosting dose of an HIV immunogen, whereinthe immunogen in each dose can be the same or different, provided thatat least one of the immunogens is an AFP of the invention, or is anucleic acid or an expression vector encoding the AFP, wherein theimmunogens are administered in an amount or expressed at a levelsufficient to induce an HIV-specific T-cell immune response in thesubject.

The interval between each dose can be at least two weeks or at leastfour weeks. Preferably, pTHr.HIVCON is administered one or more times asa priming dose and MVA.HIVCON is administered one or more times as aboosting dose. An alternative embodiment comprises administering twopriming doses and administering two boosting doses, wherein theimmunogen used for the priming doses is a plasmid vector and theimmunogen used for the boosting doses is a viral vector. The viralvector can be an MVA vector. Each of the priming doses can be a mixtureof vectors selected from the group consisting of pTHr.HIVA, pTHr.RENTA,and pTHr.HIVCON and each of the boosting doses can be a mixture ofvectors selected from the group consisting of MVA.RENTA, MVA.HIVA, andMVA.HIVCON.

Another aspect of the invention provides immunogenic compositionscomprising an AFP of the invention, or a nucleic acid encoding the AFP,or an expression vector encoding the AFP; and a pharmaceuticallyacceptable carrier. The compositions may further comprise an adjuvantselected from the group consisting of mineral salts, polynucleotides,polyarginines, ISCOMs, saponins, monophosphoryl lipid A, imiquimod,CCR-5 inhibitors, toxins, polyphosphazenes, cytokines, immunoregulatoryproteins, immunostimulatory fusion proteins, co-stimulatory molecules,and combinations thereof. Such compositions may be useful as vaccinesagainst HIV. The nucleic acids and vectors of the invention may beparticularly useful for providing genetic vaccines, i.e. vaccines fordelivering the nucleic acids encoding the AFPs of the present inventionto a subject such as a human, such that the AFPS are then expressed inthe subject to elicit an immune response.

The present invention also provides a library of immunogenicpolypeptides, comprising a plurality of polypeptides comprising at least8-15 successive amino acids of SEQ ID NO: 2 or SEQ ID NO: 4, whereineach immunogenic polypeptide corresponds to at least a portion orfragment of SEQ ID NO: 2 or SEQ ID NO: 4. In one embodiment, theplurality of immunogenic polypeptides correspond in total to the entirelength of SEQ ID NO: 2 or SEQ ID NO: 4. Preferably, a portion of eachpolypeptide in the library comprises overlapping amino acid sequences,particularly by at least eleven amino acids.

Yet another aspect of the invention provides a method of identifying aCTL epitope against HIV from the library of immunogenic polypeptides ofthe invention in a cell expressing MHC Class I protein, which maycomprise the steps of contacting the cell with the library of theinvention, selectively binding the library with the MHC protein of thecell, isolating a polypeptide of the library that selectively binds toMHC, and sequencing the polypeptide, thereby identifying the CTLepitope. The cell may be an antigen-presenting cell, preferably asplenocyte. The cell may be a human cell. When the cell is a human cell,the MHC Class I protein is human leukocyte antigen (HLA). In oneembodiment, selective binding is measured by flow cytometry. In anotherembodiment, the polypeptide is isolated by chromatography.

It is noted that in this disclosure and particularly in the claimsand/or paragraphs, terms such as “comprises”, “comprised”, “comprising”and the like can have the meaning attributed to it in U.S. Patent law;e.g., they can mean “includes”, “included”, “including”, and the like;and that terms such as “consisting essentially of” and “consistsessentially of” have the meaning ascribed to them in U.S. Patent law,e.g., they allow for elements not explicitly recited, but excludeelements that are found in the prior art or that affect a basic or novelcharacteristic of the invention.

These and other embodiments are disclosed or are obvious from andencompassed by, the following Detailed Description.

BRIEF DESCRIPTION OF THE DRAWINGS

The following Detailed Description, given by way of example, but notintended to limit the invention to the specific embodiments described,may be best understood in conjunction with the accompanying Figures.

FIG. 1 is a schematic representation of the HIVCON immunogen. The HIVCONimmunogen is a chimeric protein derived from highly conserved domains ofHIV proteins. The gene of origin for each sequence domain is shown inthe box, while the Clade of origin (of the consensus sequence) is shownbelow. Ga=Gag; Po=Pol; Vi=Vif; En=Env. The version of HIVCON shown inthe figure also has one monkey CTL epitope (Mamu), one mouse CTL epitope(P18-I10, discussed below and indicated as H-2 in the schematic) and amonoclonal antibody (mAb) epitope (Pk) following the last Env domain.Other versions of the HIVCON immunogen, as described herein, may nothave these last three additional domains, and instead terminate at thelast Env domain.

FIG. 2 is the nucleotide sequence of SEQ ID NO. 1, a 2334 nucleotidesequence that encodes an HIVCON immunogen that does not comprise thethree additional epiptopes (monkey CTL epitope (Mamu), mouse CTL epitope(P18-I10/H2) and mAb epitope Pk) following the last Env domain. SEQ IDNO. 1 starts at the first ATG (encoding the first methionine) andterminates with a stop codon (TAG) after the nucleotides encoding thelast amino acid of the last Env domain.

FIG. 3 is the amino acid sequence of SEQ ID NO. 2, the 777 amino acidimmunogen encoded by SEQ ID NO. 1. This HIVCON immunogen does notcomprise the three additional epiptopes (monkey CTL epitope (Mamu),mouse CTL epitope (P18-I10/H2) and mAb epitope Pk) following the lastEnv domain.

FIG. 4 is the nucleotide sequence of SEQ ID NO. 3, a 2421 by nucleotidesequence that encodes an HIVCON immunogen comprising a monkey CTLepitope (Mamu), a mouse CTL epitope (P18-I10/H2) and a mAb epitope (Pk)following the last Env domain. The first 2331 nucleotides are the sameas the 2331 coding nucleotides of SEQ ID NO.1 (i.e. the sequence of SEQID NO. 1 without the last stop codon). The last 90 nucleotides are thosethat encode the monkey CTL epitope (Mamu), the mouse CTL epitope(P18-I10/H2) and the mAb epitope (Pk).

FIG. 5 is the amino acid sequence of SEQ ID NO. 4, an 806 amino acidimmunogen that encodes an HIVCON immunogen comprising a monkey CTLepitope (Mamu), a mouse CTL epitope (P18-I10/H2) and a mAb epitope (Pk)following the last Env domain. The first 777 amino acids arc the same asSEQ ID NO.2. The last 29 amino acids arc those that encode the monkeyCTL epitope (Mamu), the mouse CTL epitope (P18-I10/H2) and the mAbepitope (Pk).

FIG. 6 is the nucleotide sequence of SEQ ID NO. 5, 2382 nucleotidesequence encoding an HIVCON immunogen. The first 18 nucleotides comprisetwo restriction sites (a SmaI/XmaI site and a XbaI site). These sitescan be used to insert/remove the HIVCON coding sequence into vectorssuch as the pTH or pTHr vectors described herein. The next 12nucleotides comprise the Kozak consensus leader sequence CACCATG(underlined). Nucleotides 30-2364 are the HIVCON coding sequence of FIG.2 (SEQ ID NO: 1) and encode the HIVCON immunogen of FIG. 3 (SEQ ID NO.4)—i.e. without the additional three epitopes added. Nucleotides 30-2364are shown in bold typeface. The last 18 nucleotides comprise tworestriction sites (a SmaI/Xmal site and a Xbal site) that can be used toinsert/remove the HIVCON coding sequence into various vectors such asthe pTH or pTHr vectors described herein.

FIG. 7 demonstrates the expression of HIVCON and HIVCONΔH in 293T cells.The expression of the HIVCON protein from pTH.HIVCON plasmid DNA (A),pTH.HIVCONΔH plasmid DNA (B), MVA.HIVCON (C), MVA.HIVCONΔH (D) andAd.HIVCON (E) in human 293T (A, B, C and D) or HEK 293 (E) cells wasdetected using immunofluorescence and mAb to the Pk tag of HIVCON. Thenuclei are shown in blue (appears as pale gray in black & white), Pk ingreen (appears as bright/white in black and white) (A, B, C and D) orred (appears as bright/white in black and white) (E).

FIG. 8 is a killing assay that demonstrates the immunogenicity ofpTHr.HIVCON as assessed by the elicitation of T-cell responses againstthe P18-I10 epitope of HIVCON. BALB/c mice were immunized with a singledose of 100 μg DNA intramuscularly. Splenocytes were harvested after 10days, restimulated for 5 days in culture with the P18-I10 peptide andtested in a ⁵¹Cr-release assay. The figure graphically illustrates thepercentage of specific lysis as a function of effector target cell ratioin a ⁵¹Cr-release assay for mice immunized with pTHr.HIVA (left panel)or pTHr.HIVCON (right panel) using P18-I10 peptide-pulsed (solid circle)or unpulsed (open circle) target cells.

FIG. 9 shows a bar graph representation of FACS analyses of thepercentages of CD8+ splenocytes producing IFN-γ among mouse splenocytesisolated from mice treated with HIVA or HIVCON immunogen and stimulated(filled bars) or unstimulated (open bars) with P18-I10 peptide.

FIG. 10 shows the results of in vitro proliferation assay. BALB/c micewere immunized with a single dose of 100 μg DNA intramuscularly.Splenocytes were harvested after 10 days, stained with CFSE andrestimulated for 5 days in culture with the P 18-I10 peptide andanalyzed on a FACS Calibur. FACS data acquisition was gated onlymphocytes and CD8+ populations. Data from representative mice isshown.

FIG. 11. Immunogenicity of HIVCON vaccines in BALB/c mice. (A)Immunogenicities of the individual vaccine compotents. Splenocytes fromindividual animals were tested ex vivo for the production of IFN-γ in anELISPOT assay using the RGPGRAFVTI epitope. (B) As for A, but withhigher doses for the MVA.HIVCON and Ad.HIVCON vaccines. (C)Immunogenicities of individual vaccine components compared to variousprime-boost vaccination regimes, using an IFN-γ ELISPOT assay as above.(D) Immunogenicities of individual vaccine components compared to a DNAprime-MVA boost vaccination regime. Splenocytes from individual animalswere restimulated for 5 days in culture with the RGPGRAFVTI peptide andtested in a ⁵¹Cr-release assay on peptide pulsed (full) or unpulsed(open) targets.

FIG. 12. Immunogenicity of the HIVCON and HIVCONΔH vaccines in BALB/cmice. (A) Splenocytes from individual animals were tested ex vivo forthe production of IFN-γ in an ELISPOT assay using pools of overlappingpeptides spanning the entire HIVCON sequence. Animals were immunizedwith 100 μg of pTH.HIVCON at 0 weeks, 10⁸ PFU of Ad.HIVCON at 2 weeks,and 10⁷ PFU of MVA.HIVCON at 8 weeks. Animals were sacrificed at 10weeks. (B) As for (A), but using animals immunized with 100 μg ofpTH.HIVCONΔH at 0 weeks and 10⁷ PFU of MVA.HIVCONμH at 2 weeks. Animalswere sacrificed at 4 weeks. The reactive peptides in pools 1, 3 and 4were identified.

FIG. 13. Immunogenicity of the HIVCON vaccine in HLA-A2 transgenic miceHHD. Splenocytes from individual HHD animals were tested ex vivo for theproduction of IFN-γ in an ELISPOT assay using pools of overlappingpeptides spanning the entire HIVCON sequence. Animals were immunizedwith 100 μg of pTH.HIVCON at week 0, 10⁸ PFU of Ad.HIVCON at week 2, and10⁷ PFU of MVA.HIVCON at week 8. Animals were sacrificed at week 10.Reactive peptides in pools 3 and 4 were identified.

DETAILED DESCRIPTION OF THE INVENTION

An “immunogen” refers to a substance that is recognized by the immunesystem and induces an immune response. A similar term used in thiscontext is “antigen”.

A “subject” in the context of the present invention may be a vertebrate,such as a mammal, bird, reptile, amphibian or fish; more advantageouslya human, or a companion or domesticated or food-producing orfeed-producing or livestock or game or racing or sport animal such as acow, a dog, a cat, a goat, a sheep or a pig or a horse, or even fowlsuch as turkey, ducks or chicken. Preferably, the vertebrate is a human.

The terms “protein”, “peptide”, “polypeptide” and “polypeptide fragment”may be used interchangeably herein to refer to polymers of amino acidresidues of any length. The polymer may be linear or branched, it maycomprise modified amino acids or amino acid analogs, and it may beinterrupted by chemical moieties other than amino acids. The terms alsoencompass an amino acid polymer that has been modified naturally or byintervention; for example disulfide bond formation, glycosylation,lipidation, acetylation, phosphorylation, or any other manipulation ormodification, such as conjugation with a labeling or bioactivecomponent.

An “isolated” polynucleotide or polypeptide may be one that issubstantially free of the materials with which it is associated in itsnative environment. By substantially free, is meant at least 50%,advantageously at least 70%, more advantageously at least 80%, and evenmore advantageously at least 90% free of these materials.

The present invention relates to AFPs for promoting immune responses toHIV in a human subject. These AFPs are non-naturally occurring proteinsthat comprise multiple HIV domains. The AFPs of the invention canoptionally comprise one or more additional domains useful for monitoringexpression levels of an AFP in cells or laboratory animals and/or immuneresponses to the AFP in laboratory animals.

In particular, the AFPs of the invention comprise Gag, Pol, Vif, and Envsequences. These sequences encompass (a) an HIV Gag domain, (b) one ormore HIV Pol domains; (C) an HIV Vif domain; and (d) one or more HIV Envdomains. The amino acid sequence of the HIV domains can be selected sothat the AFP predominantly induces an immune response to apre-determined HIV Clade. For example, if an immune response against HIVClade A is desired, then the amino acid sequences for Gag, Pol, Vif, andEnv are preferably the Clade A consensus sequences for each of thoseproteins. Preferably, the AFPs of the invention comprise HIV domainsthat are selected from among several different Clades, so as to providea cross-Glade or Glade-universal immunogen against HIV.

More particularly, an “artificial fusion protein” or “AFP” as usedherein is a protein or polypeptide (these terms are usedinterchangeably) which does not naturally occur in nature, i.e., AFPsare the product of a design process and the entire AFP as designed isnot naturally encoded in the genome of an organism. An AFP of theinvention must have at least two distinct protein domains arranged in anon-naturally occurring manner, i.e., the two domains are arranged (orfused together) in a manner not normally found in a single protein. Fordomains originating from different proteins, the arrangement (or orderof joining) is flexible. If the two domains are from the same protein orfrom a single polyprotein, such as a viral polyprotein, the domains arejoined together in a manner to provide a primary linear structuralarrangement that differs from the original primary structure associatedwith those domains, as they are encoded in the protein is in the genomeof the organism from which the domains are derived. For example,contiguous domains from a single protein can be joined in reverse orderor can be separated by an intervening domain. For example, an AFP couldbe made by figuratively cutting a protein in half and reordering thecoding sequence for (or fusing) the fragments so that the sequencenormally found at the carboxy end of the protein is now at the aminoterminus of the AFP and the original amino-terminal amino acid is in themiddle of the protein.

The domains of the AFPs can be joined by any means, including, withoutlimitation, by covalent bonds, such as a peptide bond or via insertionof a chemical linker, or by non-covalent bonds, such as an ionic bond.Preferably, the domains of the AFPs are joined by covalent bonds. Asused herein, “domain” means a region or sequence of amino acids from aprotein or polypeptide without regard to whether that region or sequenceforms a particular structural or functional unit. A “domain” can alsocomprise one or more “subdomains”, which can comprise parts of proteins,or fragments of proteins or peptides. However, the selection ofparticular amino acids as a domain or subdomain does not preclude thatdomain or subdomain from also being a structural and/or functional unitof the protein or polypeptide or from having been selected on the basisof its structure or function.

The size of the domain can vary from a few (less than 10) to manyhundreds of amino acids, with the actual domain size based on the reasonthat particular domain is included in the AFP. For example, a domainthat serves as a spacer may range from 2-3 amino acids to 10-15 aminoacids, with the exact number of amino acids determined as needed, e.g.,to facilitate cloning sites, to avoid frameshifts in the reading framesof the coding sequences, to provide a particular distance betweendomains, or for any combination of these or other reasons. As anotherexample, a domain whose function is to encode CTL epitopes may rangefrom 5-12 amino acids if a single epitope is encoded, or may be severalhundred amino acids if multiple epitopes are encoded. If desired, adomain in the AFP can consist of an entire protein or modified versionsof an entire protein, again as dictated by the reason for including thatdomain in the AFP.

The amino acid sequence of a domain is determined by the nature of theindividual domain of the present invention and described in detailbelow. In this regard, those sequences include naturally-occurringsequences, modified sequences, consensus sequences and the like.Sequence modifications can be achieved by deleting, inserting orchanging one or more amino acids. New domains can be made by changingthe normal arrangement of amino acids, e.g., by transposing differentparts of the protein.

The amino acid sequence for the Gag, Pol, Vif, and Env domains in theAFPs of the invention can be from a consensus sequence for a specificClade to preferentially generate an immune response to that specificClade. Alternatively, the amino acid sequences of the domains can beselected to generate an immune response against any of the other HIVClades, by using amino acid sequences conserved within, andcharacteristic of, the selected Clade. HIV Clades include Clades A, B,C, D. H, F, G, H, I, J, and K. Consensus sequences from CRFs can also beused.

The simplest form of a consensus sequence can be created by selectingthe most frequent amino acid at each position of a protein in a set ofaligned protein sequences. Thus, as the number of proteins beingcompared increases, the consensus sequence can also change. Theconsensus sequence for HIV proteins from different clades is regularlyupdated by the Los Alamos HIV database and is readily available to thepublic. While these compilations may evolve over time as additionalisolates of HIV are analyzed and as Clade groupings are altered, thisevolution does not affect the use of consensus sequences in the presentinvention. Any of these published consensus sequences or any consensussequence derived from a desired group of sequences can be used in theinvention.

To select the equivalent, corresponding, or correlating amino acids forthe domains of the invention (these terms are used interchangeably), oneof skill in the art can align the candidate HIV isolate or consensussequence with the indicated amino acids of SEQ ID. NO: 2 and therebydetermine the corresponding sequence, making allowances for deletionsand insertions of amino acids in that region of sequence. It is wellknown that such alignments may not yield precisely the same length ofamino acid sequences due to well known HTV variation. Consequently, thedomains for equivalent sequences generally vary in size from 1 to 15amino acids (or fewer, preferably from 1-10 or 1-5 amino acids and morepreferably 1, 2 or 3 amino acids) to accommodate small insertions anddeletions. Such insertions and deletions can occur within or at the endsof the equivalent sequence, provided that such length alterations arethose one of skill in the art would obtain in maximizing the alignmentbetween the candidate HIV sequence and the indicated portions of SEQ IDNO: 1. Alignment techniques, including manual methods or computerizedalgorithms, arc known to those of skill in the art (Altschul, S. F. etal. (1990) J. Mol. Biol. 215: 403-410).

The domains of the AFPs can be arranged in a variety of different ways(e.g., in a linear order from N- to C-terminus or via chemicalcrosslinking) without significantly affecting the immunogenic characterof the AFP. Accordingly, the AFPs can have the domains arranged in anyorder that preserves immunogenicity, preserves the requiredcharacteristics of the individual domains (e.g., abolishes the relevantbiological activity), and does not recreate a naturally-occurringprotein.

The AFPs can be synthesized by conventional chemical techniques, such assolid phase synthesis or produced by recombinant DNA technology,preferably the latter. Individually-produced domains can be purified andjoined by chemical cross-linking or any other method known in the art.Methods of synthesis, recombinant DNA techniques to produce proteins andchemical cross-linking methods are well known to those of skill in theart. Hence, the invention includes methods of preparing AFPs byculturing a host cell containing an expression vector of the invention(see below) for a time and under conditions sufficient to express theAFP, and recovering the AFP. Methods useful to recover, and/or purifythe AFP to homogeneity can be determined by those of skill in the art.Such methods include cesium chloride centrifugation, oligonucleotideaffinity chromatography, ethanol precipitation, among others.

The domains and intervening sequences of the AFPs of the invention aredescribed in detail below. A description of HIVCON, a preferredembodiment of the present invention, is also described below. The HIVGag domain of the AFPs preferably comprise three subdomains, but cancontain one, two, or any number of subdomains, provided that the Gagsequences do not form a naturally-occurring protein. The HIV Gagsubdomains preferably correlate to sequences of the most highlyconserved regions of the Gag protein among the four most prevalent HIVclades A-D, with less than about 6% variability across HIV Clades A-D.The HIV Gag sequences need not contain dominant CTL epitopes, howeverthe skilled artisan can readily identify and incorporate sequences thatare rich in dominant CTL epitopes, so as to elicit or stimulate atargeted cell-mediated immune response. Without wanting to be bound bytheory, it is believed that the presence of subdominant epitopes mayelicit or stimulate a protective immune response, possibly withoutinducing the immunodominance effect observed with the use of dominantepitopes. In a preferred embodiment, the HIV Gag sequences of theinvention arc selected irrespective of the presence or abundance ofdominant CTL epitopes.

The HIV Gag sequences can also be selected from the same Clade, therebytargeting the AFP of the invention to a specific target population wherea particular Clade is prevalent. The HIV Gag domain can comprise one ormore Gag subdomains that comprise sequences that exhibit more or lessthan about 6% variability across Clades. The Gag sequences can differ byabout 0-10%, preferably about 0-8%, and more preferably, about 0-6%. AnyHIV Gag sequence can be used in the AFPs of the invention, provided thatthe Gag sequences are highly conserved and exhibit the desiredvariability among the HIV clades and target population to be delivered,as well as preserving the desired immunogenicity. Additionally, the HIVGag sequence should not be configured or positioned in the AFP to createa naturally-occurring Gag protein.

HIVCON, a preferred embodiment of the invention, comprises an HIV Gagdomain having amino acids 1-135 of SEQ ID NO: 2 or SEQ ID NO: 4. The HIVGag domain of the invention comprises three subdomains in HIVCON. Eachof the three Gag subdomains in HIVCON comprise the following aminoacids: Gag subdomain 1 comprises amino acids 1-56 of SEQ ID NO: 2 or SEQID NO: 4; Gag subdomain 2 comprises amino acids 57-96 of SEQ ID NO: 2 orSEQ ID NO: 4; and Gag subdomain 3 comprises amino acids 97-135 of SEQ IDNO: 2 or SEQ ID NO: 4 (see also Table 1). The AFPs of the presentinvention preferably comprise three Pol domains, but can include anynumber of domains (and accordingly, subdomains within the domains), solong as the Pol sequences selected do not form a naturally-occurringprotein, or additionally or alternatively, provided that the sequencesretain their desired immunogenicity and provided that the sequences donot restore Pol enzymatic activity. Such enzymatic activity includesreverse transcriptase, integrase, protease, and RNase H. The first andsecond Pol domains each preferably comprise two Pol subdomains, whilethe third Pol domain preferably comprises four Pol subdomains. The Polsequences preferably correlate to sequences that arc the most highlyconserved and which differ by less than 6% across HIV clades A-D. TheHIV Pol domains need not contain dominant CTL epitopes, however theinvention also contemplates selecting sequences that are rich indominant CTL epitopes. Preferably, the HIV Pol domains are selectedirrespective of the presence or abundance of dominant CTL epitopes.

The HIV Pol sequences can also be selected from the same Clade and/orCRF, thereby targeting the AFP of the invention to a specific targetpopulation. Alternatively, the HIV Pol sequences can also be selectedfrom different Clades or CRFs. The HIV Pol domains can comprise one ormore Gag subdomains that comprise sequences that exhibit more or lessthan about 6% variability across HIV clades. The HIV Pol sequence candiffer by about 0-10%, preferably about 0-8%, and more preferably, about0-6%. Any HIV Pol sequence can be used in the AFPs of the invention,provided that the HIV Pol sequences are highly conserved and exhibit thedesired variability among the HIV clades and target population to bedelivered. Additionally, the selected HIV Pol sequences should lackenzymatic activity of one or all of protease, integrase, RNase, andreverse transcriptase.

HIVCON, a preferred embodiment of the invention, comprises three HIV Poldomains corresponding to: the first Pol domain comprises two subdomainscorrelating to amino acids 136-393 of SEQ ID NO: 2 or SEQ ID NO: 4; thesecond Pol domain comprises two subdomains correlating to amino acids422-484 of SEQ ID NO: 2 or SEQ ID NO: 4; and the third Pol domaincomprises four subdomains correlating to amino acids 522-723 of SEQ IDNO: 2 or SEQ ID NO: 4. The amino acids of each Pol subdomain arecollectively shown in Table 1.

The HIV Vif domain of the AFPs of the present invention are preferablyselected from sequences of the most highly conserved region or regionsof Vif among the four most prevalent HIV clades A-D, with less thanabout 6% variability across clades. The HIV Vif sequence need notcontain dominant CTL epitopes, and alternatively may comprisesubdominant CTL epitopes. One of skill in the art can readily substituteregions of Vif that are rich in dominant CTL epitopes in order to targeta cell-mediated immune response in a particular target population.Preferably, the HIV Vif sequence of the invention is selectedirrespective of the presence or abundance of dominant CTL epitopes.

The HIV Vif sequence can be selected from across divergent HIV Cladesand CRFs, in comparison to the other HIV sequences present in the AFPsof the invention. The HIV Vif domain can comprise sequences that exhibitmore or less than about 6% variability across HIV clades. Preferably,the HIV Vif sequence differ by about 0-10%, preferably about 0-8%, andmore preferably, about 0-6%. Any HIV Vif sequence can be used in theAFPs of the invention, provided that the Vif sequence is highlyconserved and exhibit the desired variability among the HIV clades andtarget population to be delivered. The selected HIV Vif sequence shouldalso preserve the desired immunogenicity.

A preferred embodiment of the invention, HIVCON, comprises an HIV Vifdomain having amino acids 394-421 of SEQ ID NO: 2 or SEQ ID NO: 4 (Table1).

The AFPs of the present invention preferably comprise at least two Envdomains. The Env domains preferably correlate to sequences that are themost highly conserved and which exhibit less than 6% variability acrossHIV Clades A-D. The HIV Env domains need not contain dominant CTLepitopes, however the invention also contemplates selecting Envsequences that are rich in dominant CTL epitopes. Such a substitutioncould result in an enhanced cell-mediated immune response that can betargeted to a specific population where a particular Clade or CRF ispredominant. Preferably, the HIV Env domains are selected irrespectiveof the presence or abundance of dominant CTL epitopes.

When designing an AFP that is targeted to a specific HIV Clade, the HIVEnv sequences can also be selected from that HIV Clade or CRF, therebytargeting the AFP of the present invention to a specific targetpopulation. The HIV Env sequences can comprise sequences that exhibitless than about 6% variability across HIV Clades. The Env sequences candiffer by about 0-10%, preferably about 0-8%, and more preferably, about0-6%. Any HIV Env sequence can be used in the AFPs of the invention,with the proviso that the Env sequences are highly conserved and exhibitthe desired variability among the HIV Clades and target population to bedelivered, as well as preserve the desired immunogenicity.

Table 1 depicts each HIV domain of HIVCON, a preferred embodiment of thepresent invention, including subdomains of each domain, and theappropriate amino acids corresponding to SEQ ID NO: 2. The same aminoacid sequences are are found at the same positions in SEQ ID NO:2.

TABLE 1 HIV domains of HIVCON Amino Acid of Domain Subdomain SEQ ID NO:2 Clade Gag 1 a.a. 1-56 C 2 a.a. 57-96 D 3 a.a. 97-135 A Pol Domain 1 1a.a. 136-265 B 2 a.a. 266-393 C Pol Domain 2 1 a.a. 422-457 A 2 a.a.458-484 B Pol Domain 3 1 a.a. 522-556 D 2 a.a. 557-629 A 3 a.a. 630-676B 4 a.a. 677-723 C Vif — a.a. 394-421 D Env Domain 1 — a.a. 485-521 CEnv Domain 2 — a.a. 724-777 D

The AFPs of the invention can have additional, non-HIV domains to aid incharacterization and monitoring of the AFP. Preferably such domains areat the N and/or C-termini of the AFP, but they can also be interposedbetween the HIV domains of the AFP. For example, the additional domainscan encode intra- or extracellular signals or sites that affectprocessing of the polypeptide (e.g., to include a protease cleavagesite, signal sequence for intracellular localization or trafficking, orother such sequence), sites to aid protein purification and/or sites toaid protein localization. Sites useful for protein purification orlocalization include sequences that enable affinity binding. Forexample, epitopes recognized by antibodies (including, but not limitedto, Pk, Flag, HA, myc, GST or His) that are well known in the art can beincluded (Harlow et al., Using Antibodies: A Laboratory Manual, ColdSpring Harbor Laboratory Press, 1998). In certain embodiments of theinvention, such as in the HIVCON immunogen of SEQ ID NO:4, the Pkepitope tag is used. This is an epitope bound by a monoclonal antibody(mAB). The epitope is referred to either as Pk or Pk tag (from mAb clone“k”) and is from the SV5 virus phosphoprotein P. The amino acid sequenceof the Pk epitope is IPNPLLGLD (SEQ ID NO:6), and is the last 9 aminoacids (amino acids 798-806) of SEQ ID NO:4. The additional domains canalso be immunogenic in a laboratory animal (e.g., simian or murine CTLepitopes) and thereby provide an additional method of monitoring the AFPduring developmental research, preclinical studies and possibly, duringclinical use. When such additional immunogenic domains are used, thenumber of such domains should be minimized, preferably to no more than 3or 4, to avoid interference with or competition for stimulation ofHIV-specific immune responses.

In a preferred embodiment, the AFPs have a domain with at least onenon-human CTL epitope that is recognized by the immune system of one ormore laboratory animals, such as mice, non-human primates (includingchimpanzees, rhesus macaques and other monkeys and the like), rabbits,rats, or other suitable laboratory animals. Major histocompatibilitycomplex (MHC) molecules present these epitope peptides to T cells. Forrhesus macaque (Macaca mulata), the MHC molecule is referred to as Mamu,for mice it is historically referred to as H-2, and for humans it isreferred to as HLA. Inclusion of a non-human CTL epitope allowsassessment of the quality, reproducibility, and/or stability ofdifferent batches of the AFPs using a laboratory test animal. Examplesof such epitopes include the amino acid sequence STPESANL (SEQ IDNO:7)which is a Mamu-A*01-restricted epitope from simianimmunodeficiency virus (SIV) tat protein that is recognized by rhesusmonkey CTLs (hereinafter “the SIV tat CTL epitope”; Allen et al.,(2000b) Nature 407:386-390). Another example is SYIPSAEKI (SEQ ID NO:8)which is a murine H-2K^(d)-restricted CTL epitope from Plasmodiumberghei and is also called the pb9 epitope (Romero et al., (1989) Nature341: 323-326). Other suitable epitopes are known, e.g., the amino acidsequence ACTPYDINQML (SEQ ID NO:9), which contains an epitope from SIVGag p27 recognized by rhesus macaque monkey CTLs (referred to herein as“the SIV Gag p27 epitope”). The ACTPYDINQML (SEQ ID N0:9) epitope ispresent in the HIVCON immunogen of SEQ ID NO:4 (amino acid positions778-788. See FIG. 5). Another suitable epitope is CTPYDINQM (SEQ IDNO:10) (p11C, C-M)—the SIV gag p27 epitope presented to CD8 T cells bythe the Mamu-A*01 MHC. The CTPYDINQM (SEQ ID NO:10) epitope is presentin the HIVCON immunogen of SEQ ID NO:4 (amino acid positions 779-787.See FIG. 5). Another suitable epitope has the sequence RGPGRAFVTI (SEQID NO:11), a murine H-2^(k)-restricted CTL epitope from HIV gp41 proteinwhich is also known as the P18-I10 epitope, and referred to herein as“the P18-I10 epitope”. The RGPGRAFVTI (SEQ ID NO:11) epitope is presentin the HIVCON immunogen of SEQ ID NO:4 (amino acid positions 790-798.See FIG. 5). Suitable non-human CTL epitopes are known or can be readilydetermined by those of skill in the art using techniques known foridentifying CTL in laboratory animals.

The AFPs can also comprise a domain that is a small tag or marker toallow for detection of expression, localization, quantification of theamount of AFP and/or purification of the AFP. Suitable tags include, butare not limited to, epitopes recognized by mAbs, such as the epitopeIPNPLLGLD (SEQ ID NO:6) recognized by the Pk mAb (Hanke et al., (1992)J. Gen. Virol. 73:653-660). The IPNPLLGLD (SEQ ID NO:6) epitope ispresent in the HIVCON immunogen of SEQ ID NO:4 (amino acid positions799-8-6. See FIG. 5). Other suitable tags include the epitope YPYDVPDYA(SEQ ID NO:12) recognized by HA antibody; the epitope DYKDDDDK (SEQ IDNO:13) recognized by Flag antibody; the epitope YTDIEMNRLGK (SEQ IDNO:14) recognized by the VSV-G Tag antibody and the epitope EYMPME (SEQID NO:15) recognized by the Glu-Glu antibody. Those of skill in the artcan readily select suitable tags and markers for inclusion in an AFP.

The HIV domains of the AFPs can be contiguous within the protein.Alternatively, they can be separated by intervening amino acidsequences. The intervening amino acid sequences are generally non-HIVsequences, but can also comprise a small number of additional HIV aminoacids. Intervening sequences, if present, range from 1-20 amino acidsper intervening sequence domain and are preferably less than 10 aminoacids, and even more preferably from 2-5 amino acids in length. Forexample, intervening sequences can be linkers, spacers or othersequences that optimize the expression levels of the AFPs. Theintervening sequences can be used to optimize immunogenicity.Intervening sequences can also be added as a convenience to allowinclusion of useful restriction sites or to ensure that the domains ofthe AFPs are joined “in-frame” (e.g., for recombinantly-produced AFPs).

One example of an AFP of the invention is HIVCON. HIVCON is an AFPhaving 777 amino acids with 7 HIV domains (SEQ ID NO: 2, FIG. 3) andoptionally, three additional domains (as in SEQ ID NO: 4, FIG. 5). Aschematic diagram of HIVCON is shown in FIG. 1. The HIVCON protein, fromamino to carboxyl terminus, comprises an HIV Gag domain, a first HIV Poldomain (comprising two HIV Pol subdomains), an HIV Vif domain, a secondHIV Pol domain (comprising two HIV Pol subdomains), a first HIV Envdomain, a third HIV Pol domain (comprising four HIV Pol subdomains), asecond HIV Env domain, and optionally, the SIV p27 CTL epitope, themurine CTL epitope P10-I18, and the mAb epitope Pk. HIVCON does notcontain intervening sequences. The correlation of domains for the 806amino acids of HIVCON SEQ ID NO:4 (and SEQ ID NO:2 with the exception ofthe last three domains) are as follows, from N-terminus to C-terminus:

-   -   amino acids 1-135, the HIV Gag domain;    -   amino acids 136-393, the first HIV Pol domain (including both        subdomains);    -   amino acids 394-421, the HIV Vif domain;    -   amino acids 422-484, the second HIV Pol domain (including both        subdomains);    -   amino acids 485-521, the first HIV Env domain;    -   amino acids 522-723, the third HIV Pol domain (including all        four subdomains);    -   amino acids 724-777, the second HIV Env domain;    -   amino acids 778-788, the SIV Gag p27 CTL epitope;    -   amino acids 789-798, the murine CTL epitope P18-I10; and    -   amino acids 799-806, the mAb epitope Pk.

The HIV domains in HIVCON are from HIV-1 Clades A-D consensus sequences.The corresponding amino acids to each domain, including each subdomainwithin each domain, as well as their corresponding HIV Clade, is shownin Table 1.

Another aspect of the invention relates to polypeptides and polypeptidelibraries that comprise sequences that, in total, correspond to theentire length of the AFPs of the invention, advantageously SEQ ID NO: 2or SEQ ID NO:4. Alternatively, the polypeptide or polypeptide librariescan correspond to a portion or fragment of the AFP of the presentinvention, advantageously SEQ ID NO: 2 or SEQ ID NO:4. Polypeptidelibraries of the present invention can be used, inter alia, to delineateand further define the specific sequence or epitope of the AFP thatbinds to cellular receptors, such as major histocompatibility complex(MHC) Class I of the antigen-presenting cell. Polypeptide libraries cancomprise pools of short amino acid sequences, which can range anywherefrom a single amino acid, to as large as a hundred amino acids orlonger. However, it is well-known in the art that MHC receptorsrecognize short amino acid sequences of approximately 8-15 amino acidsin length. Therefore, it is preferable to synthesize polypeptides thatrange from 8 to 15 amino acids, preferably 15 successive amino acids, ofSEQ ID NO: 2 or SEQ ID NO:4.

Each polypeptide can be synthesized with or without overlappingsequences. In some applications, especially when a specific sequence ofan epitope is desired, the presence of overlapping sequences in thepolypeptide can ensure that the entire amino acid sequence of SEQ ID NO:2 or SEQ ID NO:4 is encompassed by the library of polypeptides. Theoverlapping sequences can comprise anywhere from one to 15 amino acids,depending on the length of the polypeptide. In a preferred embodiment ofthe present invention, each polypeptide comprises 15 successivenucleotides, wherein eleven of the amino acids are overlapping.

Synthesis of polypeptides can be either in vitro, such as by chemicalpeptide synthesis, solid phase synthesis, or through cell-free in vitrotranslation of an RNA encoding the short amino acid sequences (such as,but not limited to, rabbit reticulocyte lysate, wheat germ extract).Alternatively, the polypeptides may be synthesized recombinantly inproducer cells, from a nucleic acid sequence encoding the polypeptide ofinterest. The polypeptides can be purified by methods known in the art,such as reverse-phase high performance liquid chromatography (HPLC),affinity chromatography, immunoprecipitation if a known epitope iscontained within the polypeptide sequence and recognized by availablemonoclonal and/or polyclonal antibodies, ion exchange chromatography,ammonium sulfate or ethanol precipitation, acid extraction, anion orcation exchange chromatography, phosphocellulose chromatography,hydrophobic interaction chromatography, immuno-affinity chromatography,hydroxyapatitc chromatography, lectin chromatography, molecular sievechromatography, isoelectric focusing, gel electrophoresis, orcombinations of these methods using monitoring techniques to follow thepolypeptide at each purification step.

Each polypeptide corresponds to a specific portion or fragment of SEQ IDNO: 2 or SEQ ID NO:4, and the sum total of all of the polypeptides inthe library correspond to the entire length of SEQ ID NO: 2 or SEQ IDNO:4. This is to ensure that the entire amino acid sequence of SEQ IDNO: 2 or SEQ ID NO:4 is encompassed by the polypeptides in the library,so as to “scan” the entire amino acid sequence to identify CTL epitopesof interest. The polypeptides are synthesized and pooled according totheir sequence similarity. The pooled library of polypeptides can thenbe used to determine the specificity of the CTL response to HIV in cellsor subjects receiving the AFPs of the invention, or in infected cells orinfected subjects.

Accordingly, the present invention also provides a method of identifyinga CTL epitope against HIV from the library of polypeptides of thepresent invention, in a cell expressing MHC Class I protein, comprisingthe steps of contacting the cell with the library of the invention,selectively binding the library with the MHC protein of the cell,isolating a polypeptide of the library that selectively binds to MHC,and sequencing the polypeptide, thereby identifying the CTL epitope.

Cells useful in the methods of the invention are antigen-presentingcells. Antigen-presenting cells express MHC Class I proteins, which areprimarily involved in binding and restriction of epitopes that elicitT-lymphocyte-mediated responses to infection. MHC Class I moleculespresent peptides from pathogens, commonly viruses, to CD8+ CTLs, whichare specialized to kill any cell that they specifically recognize. Suchantigen-presenting cells include, but are not limited to, dendriticcells, macrophages, monocytes, mononuclear cells, CD8+ T-cells, andsplenocytes. The cells can be derived from a subject who is infectedwith HIV, or can be cells infected or transfected with the virus orviral sequences in vitro. Preferably, the cells have been immunized oradministered with the AFPs of the present invention. These cells thatalready received the AFP or other HTV sequence or virus are contactedwith the library of the invention, preferably under cell or tissueculture conditions. When human cells are used, the MHC Class I receptoris human leukocyte antigen, or HLA. The invention also comprehends cellsof non-human, preferably laboratory, animal species, such as, but notlimited to, monkey cells, rat cells, or murine cells that aretransiently or stably transfected with human MHC, or HLA. An example ofa laboratory animal expressing human HLA is the HHD transgenic mousedescribed in Carmon, L., et al (2002) J. Clin. Invest. 110: 453-462.Different HLA/MHC subtypes and alleles can be used to further specifythe nature of the interaction between the immunogenic polypeptides ofthe invention and the particular HLA/MHC allele that is known to bedominant in a particular population of interest. Alternatively, cellsderived from many different subjects, each expressing different allelesof MHC, can be used in the methods of the invention.

The library of the present invention is then allowed to selectively bindto the MHC Class I receptor present on the cell surface, generally byaddition of the library to the culture medium. Upon selective binding ofa particular polypeptide of the library, the polypeptide that binds toMHC Class I is isolated and sequenced, thereby identifying the CTLepitope. Selective binding of the polypeptide of interest to the MHCClass I receptor of the cell can be monitored by flow cytometry, butalso by determining the binding constant of the receptor-polypeptideinteraction. This can be achieved by standard enzyme kinetic assaysknown in the art. Preferably flow cytometry (also known in the art asfluorescence activated cell sorting; FACS) is used. A method of usingindirect FACS to measure peptide binding to cell-surface MHC receptorsis described in Carmon, L., et al (2002) J. Clin. Invest. 110: 453-462.Briefly, cells that are loaded with the polypeptide libraries of theinvention are incubated with anti-MHC antibodies. After washing, asecondary antibody with a fluorescent tag (i.e., fluoresceinisothiocyanate, among others) is bound to the anti-MHC antibody, afterwhich the amount of bound antibodies is measured by FACS analysis.

The resultant polypeptide of interest can be isolated by techniquesknown in the art, such as, but not limited to, reverse-phase HPLC,acetone precipitation, ammonium sulfate precipitation, trifluoroaceticacid precipitation, and chromatography methods discussed herein. Theisolated polypeptide is then subjected to sequencing to determine theprecise boundaries of the binding sequence to MHC. Sequencing methodsknown in the art include, without limitation, Edman degradation (alsoknown as N-terminal sequencing), tandem mass spectrometry, andmatrix-assisted laser desorption ionization (MALDI).

The invention also comprehends high-throughput automation of the methodsto identify CTL epitopes using the libraries of the present invention.The library or libraries of polypeptides can be synthesized on a solidsupport, such as cellulose or on a silicon array, for subsequentdetection of anti-MHC antibody binding by immunofluorescence. Therelative fluorescence corresponding to binding of the polypeptide to theMHC Class I receptor can be measured in an automated fashion, allowingfor efficient screening of hundreds or thousands of polypeptidesequences for suitable CTL epitopes.

The immunogenic polypeptides of the invention can also be used as animmunogen or antigen to elicit humoral responses to produce, forexample, monoclonal and polyclonal antibodies in host animals againstthe AFPs of the invention. Such host animals may include but are notlimited to rabbits, mice, and rats. Various adjuvants may be used toincrease the immunologic response, depending on the host species,including but not limited to Freund's (complete and incomplete), mineralgels such as aluminum hydroxide, surface active substances such aslysolecithin, pluronic polyols, polyanions, peptides, oil emulsions,keyhole limpet hemocyanin, dinitrophenol, and potentially useful humanadjuvants such as BCG (Bacille Calmette-Guerin) and Corynebacteriumparvum.

Another aspect of the invention relates to nucleic acid moleculesencoding AFPs of the invention. “Nucleic acid molecules” or “nucleicacid” as used herein means any deoxyribonucleic acid (DNA) orribonucleic acid (RNA), including, without limitation, messenger RNA(mRNA), DNA/RNA hybrids, or synthetic nucleic acids. The nucleic acidcan be single-stranded, or partially or completely double-stranded(duplex). Duplex nucleic acids can be homoduplex or heteroduplex. Thenucleic acid molecules of the invention have a nucleotide sequence thatencodes the AFPs and can be designed to employ codons that are used inhighly-expressed genes of the subject in which the AFP gene is expressed(or to be expressed). Typically, the nucleic acid has the entire codingsequence of the AFP as a single open reading frame (ORF), that is,without introns.

Different cells vary in their usage of particular codons. This codonbias corresponds to a bias in the relative abundance of particulartransfer RNAs (tRNAs) in a particular cell type. Many viruses, includingHIV and other lentiviruses, use a large number of rare codons and, byaltering these to correspond to commonly used mammalian codons, enhancedexpression of the immunogen in cells can be achieved. By altering thecodons in the sequence to match with the relative abundance ofcorresponding tRNAs, it is possible to increase expression of the AFP.Similarly, it is possible to decrease expression of the AFP bydeliberately choosing codons for which the corresponding tRNAs are knownto be rare in a particular cell type. Thus, an additional degree oftranslational control is available. The overall effect of codonoptimization can be, for example, an increase in viral titer, i.e. ifthe AFP is expressed from a viral vector, and improved safety in asubject. Codon usage tables are known in the art for mammalian cells, aswell as for a variety of other organisms.

In a preferred embodiment, the codons encoding the AFP are “humanized”codons, i.e., the codons are those that appear frequently in highlyexpressed human genes (Andre et al., J. Virol. 72:1497-1503, 1998)instead of those codons that are frequently used by HIV. Such codonusage provides for efficient expression of the AFPs in human cells. Inother embodiments, for example, when the AFP is expressed in bacteria,yeast or other expression system, the codon usage pattern is altered torepresent the codon bias for highly expressed genes in the organism inwhich the AFP is being expressed. Codon usage patterns are known in theliterature for highly expressed genes of many species (e.g., Nakamura etal., (1996) Nucl. Acids Res. 24: 214-215; Wang et al, (1998) Mol.Biotechnol 10: 103-106; McEwan et al. (1998) Biotechniques 24:131-136).

The nucleic acid sequence for HIVCON is provided, in alternative formswith (SEQ ID NO:3) and without (SEQ ID NO: 1 or SEQ ID NO: 5)nucleotides encoding the last three additional domains. In oneembodiment of the invention, the nucleic acid of the invention comprisesthe nucleotides encoding the HIVCON coding sequence provided in SEQ IDNO: 1 or SEQ ID NO:5 (beginning at nucleotide 1 of SEQ ID NO: 1 ornucleotide 30 of SEQ ID NO:5 and continuing to the stop codon). Inanother embodiment of the invention, the nucleic acid of the inventioncomprises the nucleotides encoding the HIVCON coding sequence providedin SEQ ID NO: 3 which includes the nucleotides including threeadditional epitopes (beginning at nucleotide 1 of SEQ ID NO: 3 andcontinuing to the stop codon). In another embodiment of the invention,the nucleic acids of the invention consists essentially of the sequencesof SEQ ID NO: 1, SEQ ID NO: 3, or SEQ ID NO: 5, as shown in FIGS. 2, 4,and 6, respectively.

Nucleic acid molecules encoding the AFPs of the invention can beincorporated into expression vectors and used to immunize subjects orused to express the protein in vitro, typically for protein productionor for RNA production.

As used herein, a “vector” is a tool that allows or facilitates thetransfer of an entity from one environment to another. By way ofexample, some vectors used in recombinant DNA techniques allow entities,such as a segment of DNA (such as a heterologous DNA or cDNA segment),to be transferred into a target cell. The present invention comprehendsrecombinant vectors that can include viral vectors, bacterial vectors,protozoan vectors, DNA plasmid vectors, or recombinants thereof.

With respect to exogenous DNA for expression in a vector (e.g., encodingan epitope of interest and/or an antigen and/or a therapeutic) anddocuments providing such exogenous DNA, as well as with respect to theexpression of transcription and/or translation factors for enhancingexpression of nucleic acid molecules, and as to terms such as “epitopeof interest”, “therapeutic”, “immune response”, “immunologicalresponse”, “protective immune response”, “immunological composition”,“immunogenic composition”, and “vaccine composition”, inter alia,reference is made to U.S. Pat. No. 5,990,091 issued Nov. 23, 1999, andWO 98/00166 and WO 99/60164, and the documents cited therein and thedocuments of record in the prosecution of that patent and those PCTapplications; all of which are incorporated herein by reference. Thus,U.S. Pat. No. 5,990,091 and WO 98/00166 and WO 99/60164 and documentscited therein and documents or record in the prosecution of that patentand those PCT applications, and other documents cited herein orotherwise incorporated herein by reference, can be consulted in thepractice of this invention; and, all exogenous nucleic acid molecules,promoters, and vectors cited therein can be used in the practice of thisinvention. In this regard, mention is also made of U.S. Pat. Nos.6,706,693; 6,716,823; 6,348,450; U.S. patent application Ser. Nos.10/424,409; 10/052,323; 10/116,963; 10/346,021; and WO9908713, publishedFeb. 25, 1999, from PCT/US98/16739.

Expression vectors are well-known in the art and for the presentinvention share the common feature of having a protein coding sequence“operably linked” to regulatory or nucleic acid control sequences thatdirect transcription and translation of the protein. As used herein, anAFP coding sequence and a nucleic acid control sequence are said to be“operably linked” when they are covalently linked in such a way as toplace the expression or transcription and/or translation of the AFPcoding sequence under the influence or control of the nucleic acidcontrol sequence. A “nucleic acid control sequence” can be any nucleicacid element, such as, but not limited to promoters, enhancers, IRES,introns, and other elements described herein that direct the expressionof a nucleic acid sequence or coding sequence that is operably linkedthereto. Two DNA sequences are said to be operably linked if inductionof a nucleic acid control sequence, such as a promoter, in the 5′ geneexpression sequence results in the transcription of the AFP sequence andif the nature of the linkage between the two DNA sequences does not (1)result in the introduction of a frame-shift mutation, (2) interfere withthe ability of the promoter region to direct the transcription of theantigen sequence, or (3) interfere with the ability of the correspondingRNA transcript to be translated into a protein. Thus, a nucleic acidcontrol sequence would be operably linked to an AFP nucleic acidsequence if the nucleic acid control sequence were capable of effectingtranscription of that AFP nucleic acid sequence, such that the resultingtranscript is translated into the desired protein or polypeptide.

The nucleic acid control sequences, such as promoters, enhancers and thelike, in the expression vectors are often heterologous with respect tothe host. The term “promoter” will be used here to refer to a group oftranscriptional control modules that arc clustered around the initiationsite for RNA polymerase 11 and that when operationally linked to an AFPlead to the expression of the AFP. Promoters are generally composed ofdiscrete functional modules, each consisting of approximately 7-20 by ofDNA, and containing one or more recognition sites for transcriptionalactivator proteins. At least one module in the promoter may function toposition the transcription start site while other modules may regulatethe frequency of transcriptional initiation. “Enhancers” may bedescribed as genetic elements that increase transcription from apromoter located at distance in the same DNA molecule. Much likepromoters, enhancers may be composed of many individual modules, each ofwhich binds to one or more transcriptional proteins. While both promoterand enhancers have the same general function of activating transcriptionin the cell, there is clear distinction between their functions.Enhancers, by definition, stimulate transcription at a distance and neednot direct transcriptional initiation at a particular site. Modules of apromoter, on the other hand, must direct transcriptional initiation froma particular site in a particular orientation.

The expression of the AFP nucleotide sequence in the expression vectorcan thus be under the control of a constitutive promoter or of aninducible promoter, which initiates transcription only when the hostcell is exposed to some particular external stimulus, such as, withoutlimitation, antibiotics such as tetracycline, hormones such as ecdysone,or heavy metals. In the case of a multicellular organism, such as ananimal, the promoter can also be specific to a particular tissue ororgan. Various promoters and enhancer elements that may be used in theconstruction of vectors as various embodiments of the invention arediscussed in U.S. Pat. No. 6,835,866, the contents of which is herebyincorporated by reference Furthermore, any promoter/enhancercombinations as per the Eukaryotic Promoter Database (EPDB) may be usedto drive the expression of AFP of the invention.

Expression vectors are known and available for many organisms, includingbacteria, fungi, yeast, animals (including mammals and particularlyhumans), birds, insects, plants and the like. Animals include, but arenot limited to, mammals (humans, primates, etc.), commercial or farmanimals (fish, chickens, cows, cattle, pigs, sheep, goats, turkeys,etc.), research animals (mice, rats, rabbits, etc.) and pets (dogs,cats, parakeets and other pet birds, fish, etc.).

Accordingly, expression vectors of the present invention have the codingsequence for an AFP of the invention operably linked to transcriptionaland/or translational nucleic acid control sequences, depending onwhether protein is being expressed or RNA is being produced. Theexpression vectors of the invention are useful to achieve expression ofthe AFP or a nucleic acid encoding the AFP in a particular host cell,including production of DNA or RNA encoding the AFP. Similarly, theexpression vectors of the invention include plasmid, liposomal,microorganism and viral vectors useful to deliver the AFP (as protein ornucleic acid) to a host subject.

Expression vectors of the invention include plasmids, viral vectors,bacterial vectors, protozoal vectors, insect vectors, yeast vectors,mammalian cell vectors and the like. Whether the expression vector iscapable of replication or self-amplification depends on the vectoremployed and the reason for its selection. Such characteristics can bereadily determined by the skilled artisan when considering therequirements for expressing the AFP under the identified circumstances.

Expression vectors of the invention include those used for theexpression of the AFPs in a laboratory animal, a mammal or, preferably,a human subject. These vectors are particularly useful for immunizingthe animal, mammal or human subject to stimulate an immune responseagainst the encoded AFP. Expression vectors useful in this regardinclude bacterial vectors, viral vectors, plasmids and liposomalformulations using nucleic acid (from plasmids or viruses). Forbacterial vectors, the preferred vectors are attenuated to preventproliferation of the bacterial carrier in the host or to only allowedself-limiting proliferation that will not lead to disease or otherdetrimental pathological effect. Killed bacteria are also useful. Viralvectors are preferably attenuated or replication-defective, again toprovide safety of use in the host. Plasmids, when used, can lack anorigin of replication that functions in humans.

In certain preferred embodiments, the pTH or pTHr vectors are used. Theconstruction of the pTH vector is described in Hanke et al, 1998 Vaccine16, 426-435. pTH contains an expression efficientenhancer/promoter/intron A cassette of the human cytomegalovirus (hCMV)strain AD169 genome (Whittle et al, 1987 Protein Eng. 1, 499-505;Bebbington 1991 Methods 2, 136-145). The promoter region is followed bythe pRc/CMV (Invitrogen)-derived polylinker and polyadenylation signalof the bovine growth hormone gene. The beta-lactamase gene conferringampicillin resistance to transformed bacteria and prokaryotic origin ofdouble-stranded DNA replication Co1E1 are both derived from plasmidpUC19. The pTH vector does not contain an origin for replication inmammalian cells.

The pTHr vector is derived from pTH by deletion of thebeta-lactamase/ampicillin resistance gene. It is propagated in bacteriausing the repressor-titration system developed by Cobra PharmaceuticalsLtd. (Keele, UK), which selects plasmid-carrying bacteria without theneed for the presence of an antibiotic-resistance gene on the plasmid(See U.S. Pat. No. 5,972,708, and Williams et al, 1998 Nucl. Acids Res.26, 2120-2124). The pTHr vector is particularly well suited to use inhumans because it does not introduce into the human vaccine largenumbers of copies of an antibiotic resistance gene. Therefore, in oneembodiment the nucleotides sequences encoding the HIVCON immunogens ofthe present invention are incorporated into the pTHr vector foradministration of the vector to humans as a DNA vaccine.

Any plasmid vector safe for use in humans, mammals or laboratory animalsis contemplated for use in accordance with the present invention, aswell as any plasmid vector useful for protein purification fromprokaryotic or eukaryotic expression systems.

Viral expression vectors are well known to those skilled in the art andinclude, for example, viruses such as adenoviruses, adeno-associatedviruses (AAV), alphaviruses, retroviruses and poxviruses, includingavipox viruses, attenuated poxviruses, vaccinia viruses, andparticularly, the modified vaccinia Ankara virus (MVA; ATCC AccessionNo. VR-1566). Such viruses, when used as expression vectors are innatelynon-pathogenic in the selected host humans or have been modified torender them non-pathogenic in the selected host. For example,replication-defective adenoviruses and alphaviruses are well known andcan be used as gene delivery vectors. A preferred viral vector is MVA,which is a highly attenuated vaccinia strain which fails to replicate inmost mammalian cells (Mayr et al., (1975) Infection 105:6-14). AFPs canbe cloned into many sites of the MVA and used to immunize a subject,especially a human subject, and generate an HIV-specific immune responseagainst the encoded AFP. Useful MVA cloning sites, for example includethe thymidine kinase and deletion III loci (Chakrabarti et al., (1985)Mol. Cell. Biol. 5: 3403-3409; Meyer, H. et al (1991) J. Gen. Virol. 72:1031-8; Altenburger, W. et al (1989) Arch. Virol. 105(1-2): 15-27).

It must be noted that certain poxviruses, such as MVA, NYVAC, andavipox, can only productively replicate in or be passaged through avianspecies or avian cell lines such as, for example, chicken embryonicfibroblasts. The recombinant poxviruses harvested from avian host cells,when inoculated into a non-avian vertebrate, such as a mammal, in amanner analogous to the inoculation of mammals by vaccinia virus,produce an inoculation lesion without productive replication of theavipox virus. Despite the failure of certain poxviruses, such as MVA,NYVAC, and avipox, to productively replicate in such an inoculatednon-avian vertebrate, sufficient expression of the virus occurs so thatthe inoculated animal responds immunologically to the antigenicdeterminants of the recombinant poxvirus and also to the antigenicdeterminants encoded in exogenous genes therein. Thus, in oneembodiment, when certain poxviruses or viral vectors (as disclosedabove) are used, chicken embryonic fibroblasts are preferred as the cellpermissive for viral vector replication.

The recombinant viral vectors and recombinant viruses can containpromoters that are operably linked to the AFPs of the present invention.When contained in a poxviral vector, the promoter is advantageously ofpoxviral origin, which may be, in particular, the promoter 7.5K of thevaccinia virus, I3L poxviral promoter, 11K poxviral promoter (U.S. Pat.No. 5,017,487), 42K poxviral promoter, H6 poxviral promoter, thymidinekinase poxviral promoter, E3L poxviral promoter, K3L poxviral promoter,or a synthetic poxviral promoter. The promoter can advantageously be an“early” promoter. An “early” promoter is known in the art and is definedas a promoter that drives expression of a gene that is rapidly andtransiently expressed in the absence of de novo protein synthesis. Thepromoter can also be a “strong” or “weak” promoter. The terms “strongpromoter” and “weak promoter” are known in the art and can be defined bythe relative frequency of transcription initiation (times per minute) atthe promoter. A “strong” or “weak” promoter can also be defined by itsaffinity to poxviral RNA polymerase.

The invention also provides for viral promoters that are mutated.Without being bound by theory, it is believed that high levels ofexpression of potentially toxic heterologous sequences expressed fromviral vectors can preclude formation of stable viral recombinants.Therefore, the present invention also comprehends the use of a mutatedviral promoter, such as, for example, a mutated H6 poxviral promoteruseful when poxvirus recombinants are desired, such that the expressionlevels of the AFP sequences expressed from viral vectors are decreasedcompared with expression levels of the heterologous sequences under awild type promoter. The mutated H6 promoter can be considered a weakpromoter.

The mutated promoters can contain point mutations. The invention canalso employ promoters other than H6, which contain point mutations thatreduce their frequency of transcription initiation compared with thewild type promoter. In addition, other types of mutated promoters aresuitable for use in the instant invention (see also Davison, A. et al(1989) J. Mol. Biol. 210: 749-769; Taylor J. et al., Vaccine, 1988, 6,504-508; Guo P. et al. J. Virol., 1989, 63, 4189-4198; Perkus M. et al.,J. Virol., 1989, 63, 3829-3836).

The viral vectors or viruses of the present invention can furthercomprise additional sequences to control transcription and translationof the AFPs. For example, when contained in a poxviral vector, suchsequences can comprise a T5NT termination recognition signal, which canbe recognized by poxviral RNA polymerase for termination of early RNAtranscription.

The AFPs of the invention can also be delivered as adenovirusrecombinants, which include E1-defective or deleted, E3-defective ordeleted, and/or E4-defective or deleted adenovirus vectors, or the“gutless” adenovirus vector in which all viral genes are deleted. Theadenovirus vectors can comprise mutations in E1, E3, or E4 genes, ordeletions in these or all adenoviral genes. The E1 mutation raises thesafety margin of the vector because E1-defective adenovirus mutants aresaid to be replication-defective in non-permissive cells, and are, atthe very least, highly attenuated. The E3 mutation enhances theimmunogenicity of the antigen by disrupting the mechanism wherebyadenovirus down-regulates MHC class I molecules. The E4 mutation reducesthe immunogenicity of the adenovirus vector by suppressing the late geneexpression, thus may allow repeated re-vaccination utilizing the samevector. The present invention comprehends adenovirus vectors that aredeleted or mutated in E1, E3, E4, E1 and E3, and E1 and E4. The presentinvention also comprehends adenoviruses of the human Ad5 strain.

The “gutless” adenovirus vector can also be used to express AFPs of thepresent invention. Its replication requires a helper virus and a specialhuman 293 cell line expressing both E1a and Cre, a condition that doesnot exist in natural environment; the vector is deprived of all viralgenes, thus the vector as a vaccine carrier is non-immunogenic and maybe inoculated multiple times for re-vaccination. The “gutless”adenovirus vector also contains 36 kb space for accommodatingtransgenes, thus allowing co-delivery of a large number of heterologousgenes into cells. Specific sequence motifs such as the RGD motif may beinserted into the H-I loop of an adenovirus vector to enhance itsinfectivity. This sequence has been shown to be essential for theinteraction of certain extracellular matrix and adhesion proteins with asuperfamily of cell-surface receptors called integrins. Insertion of theRGD motif may be advantageously useful in immunocompromised subjects. Anadenovirus recombinant is constructed by cloning specific transgenes orfragments of transgenes into any of the adenovirus vectors such as thosedescribed above.

Other viral vectors useful for delivering the AFPs include alphavirusvectors, particularly those based on the replicons of Semliki ForestVirus (SFV), Sindbis virus and Venezuelan Equine Encephalitis virus(VEE) (see, e.g., Smerdou et al., (2000) Gene. Ther. Regul. 1:33-63;Lundstrom et al., (2002) Technol. Cancer Res. Treat. 1: 83-88; Hanke2003). Alphavirus replicons are useful expression vectors and can referto RNA or DNA comprising those portions of the alphavirus genomic RNAessential for transcription and export of a primary RNA transcript fromthe cell nucleus to the cytoplasm, for cytoplasmic amplification of thetransported RNA and for RNA expression of a heterologous nucleic acidsequence, such as the AFPs of the present invention. Thus, the repliconencodes and expresses those non-structural proteins needed forcytoplasmic amplification of the alphavirus RNA and expression of thesubgenomic RNA, as well as an AFP of the invention. It is furtherpreferable that the alphavirus replicon cannot be encapsidated toproduce alphavirus particles or virions. This can be achieved byreplicons, which lack one or more of the alphavirus structural genes,and preferably all of the structural genes, such as occurs with aone-helper or two-helper alphavirus vector system. In a preferredembodiment, alphavirus replicons are capable of being transcribed from aeukaryotic expression cassette and processed into RNA molecules withauthentic alphavirus-like 5′ and 3′ ends.

Alphavirus replicons and expression vectors containing them are wellknown in the art and many vectors containing a wide range of alphavirusreplicons have been described. Examples of such replicons can be found,e.g., in U.S. Pat. Nos. 5,739,026; 5,766,602; 5,789,245; 5,792,462;5,814,482; 5,843,723; and 6,531,313; and in Polo et al., (1998) NatureBiotechnol. 16: 517-518 and Berglund et al., (1998) Nature Biotechnol.16: 562-565. Alphavirus replicons can be prepared from any alphavirus orany mixture of alphavirus nucleic acid sequences. In this regard, thepreferred alphavirus replicons are derived from Sindbis virus, SFV, VEEor Ross River virus.

Other viral expression vectors include flaviviruses (WO02/072835), suchas yellow fever virus, Dengue virus and Japanese encephalitis virus,poxviruses such as vaccinia virus (U.S. Pat. No. 5,505,941),avipoxviruses such as fowlpox virus (Kent) and canarypox virus(Clements-Mann et al., (1998) J. Infect. Dis. 177: 1230-1246; Egan etal., (1995) J. Infect. Dis. 171: 1623-1627; U.S. Pat. No. 6,340,462),including attenuated avipoxviruses such as TROVAC (U.S. Pat. No.5,766,599) and ALVAC (U.S. Pat. No. 7,756,103), picornaviruses such aspoliovirus (U.S. Pat. Nos. 6,780,618; 6,255,104; WO92/014489) andrhinovirus, herpesviruses (WO87/000862; WO 87/04463; WO97/014808) suchas Varicella zoster virus (VZV; WO97/004804), NYVAC (New York vacciniavirus with 18 gene deletions selected to decrease pathogenicity) (Hel etal., (2001) J. Immunol. 167: 7180-7191; U.S. Pat. Nos. 5,494,807;5,762,938; 5,364,773); Adenovirus (AdV; WO95/02697; WO95/11984;WO95/27071; WO95/34671), adeno-associated virus (AAV; U.S. Pat. Nos.4,797,368; 5,474,935), influenza virus (WO03/068923; WO02/008434;WO00/053786), cauliflower mosaic virus (U.S. Pat. No. 4,407,956),tobacco mosaic virus (TMV) (Palmer et al, (1999) Arch. Virol. 144:1345-1360; WO93/003161) and NS1 tubules of bluetongue virus (Adler etal., (1998) Med. Microbial. Immunol. (Berl) 187: 91-96). Many of thesevectors are readily available and conditions applicable for their useare well-known to the skilled artisan.

Expression vectors of the invention also include bacterial expressionvectors for administration to a laboratory animal, mammal or humansubject. Such bacterial expression vectors (attenuated, invasivebacteria) are bacteria that contain a plasmid or an expression cassetteencoding an AFP of the invention. The expression cassette can driveexpression in the bacteria or in eukaryotic cells. In the former,expression is achieved before introducing the bacterial cells into thehost, whereas in the latter, expression occurs in the host and can bedriven by the host cellular machinery. U.S. Pat. Nos. 5,877,159;6,150,170; 6,500,419 and 6,531,313 describe bacterial vectors thatinvade animal cells without establishing a productive infection orcausing disease and thus permit the introduction of a expressioncassette encoding an AFP into a eukaryotic cell to obtain expression ofthe AFP.

Suitable bacterial expression vectors include Mycobacterium bovis,Bacillus Calmette Guerin (BCG), and attenuated strains of Salmonella(especially the “double aro” mutants of Salmonella that are beingdeveloped as vaccines for diarrheal diseases), Shigella (see Shata etal., (2000) Mol. Med. Today 6: 66-71), Neisseria and Listeriamonocytogenes. Preferred Salmonella typhi strains include CVD908Δasd,CVD908ΔhtraA and CVD915. The CVD908Δasd Salmonella strain derives fromCVD908 (Tacket et al., (1992) Vaccine 10: 443-446) by deletion of theasd gene that encodes the aspartate b-semialdehyde dehydrogenase (asd),an enzyme necessary for the synthesis of diaminopimelic acid (DAP) fromaspartate. CVD908ΔhtrA is a S. typhi strain with the htrA gene deleted.This mutation knocks out a heat shock gene that further attenuates thestrain (Tacket et al., (1997) Infect. Immunol. 65:452-456). CVD915 is anattenuated S. typhi strain that has a deletion of the guaBA locus,resulting in its attenuation (Pasctti et al., Clin. Immunol. 92:76-89,1999). This strain has been shown to be excellent for the delivery ofDNA vaccines in animal studies. A preferred Shigella strain is S.flexneri CVD 1207. This strain has deletions of the sen, set, virG andguaBA genes that renders it well attenuated while preserving itsimmunogenicity (Kotloff et al., Infect. Immunol. 68:1034-1039, 2000).

Expression vectors of the invention are also used for preparation andpurification of the AFPs of the invention. Vectors in this regard aretypically used in bacteria, yeast, insect or mammalian cells. Thenucleic acid control sequences directing expression of the nucleic acidmolecule encoding the AFP are chosen based on the host cell (e.g.,bacterial, yeast, insect or mammalian cells) from which the expressionis being directed. Appropriate nucleic acid control sequences for aparticular host cell and expression vector are well known. Theexpression vectors containing the AFP can be introduced into these cellsby well-known methods in the art, which depend, inter alia, on the typeof cell and whether the duration of expression is transient or stable.For example, calcium chloride transfection is commonly utilized forprokaryotic cells, whereas calcium phosphate treatment, lipofection,microinjection, particle bombardment, or electroporation is used formany eukaryotic cells. Any transfection, infection, transformation orsuitable technique for introducing an expression vector into a cell,whether prokaryotic or cukaryotic, known to the skilled artisan can beused.

There are numerous Escherichia coli vectors and cells known to one ofordinary skill in the art that are useful for expression of the AFPs ofthe invention. Other microbial hosts suitable for use include bacilli,such as Bacillus subtilis, and other enterobacteria, such as Salmonella,Serratia, as well as various Pseudomonas species. These prokaryotichosts can support expression vectors, which typically contain expressioncontrol sequences operable primarily in the host cell. Any number of avariety of well-known promoters can be present, such as the lactosepromoter system, a tryptophan (Trp) promoter system, a β-lactamasepromoter system, or a promoter system from phage λ. The promoters willtypically control expression, optionally with an operator sequence andhave ribosome binding site sequences for example, for initiating andcompleting transcription and translation. If necessary, anamino-terminal methionine can be provided by insertion of a Met codon 5′and in-frame with the protein. Among vectors preferred for use inbacteria include pQE70, pQE60 and pQE9, available from QIAGEN, Inc.;pBluescript vectors, Phagescript™ vectors, pNH8A, pNH16a, pNF118A,pNH46A, available from Stratagene Cloning Systems, Inc.; and ptrc99a,pKK223-3, pKK233-3, pDR540, pRIT5 available from Pharmacia Biotech, Inc.Other expression vector systems are based on β-galactosidase (p-gal;pEX), maltose binding protein (pMAL) and glutathione S-transferase(pGST) (see e.g., Smith, (1988) Gene 67: 31-40 and Abath. (1990) PeptideResearch 3: 167-168).

Yeast cells can also be used to direct expression of the AFPs of theinvention. There are several advantages to yeast expression systems thatmake use of the yeast system desirable in certain circumstances,including providing disulfide pairing, post-translational modifications,protein secretion and easy isolation when protease cleavage site isinserted upstream of from the AFP coding sequence. The Saccharomycescerevisiae pre-pro-α-factor leader region (encoded by the MFa-I gene) isroutinely used to direct protein secretion from yeast (Brake et al.,(1984) Proc. Natl. Acad. Sci. USA 82: 4642-4646; U.S. Pat. No.4,870,008). The leader region of pre-pro-α-factor contains a signalpeptide and a pro-segment, which includes a recognition sequence for ayeast protease encoded by the KEX2 gene. This enzyme cleaves theprecursor protein on the carboxyl side of a Lys-Arg dipeptidecleavage-signal sequence. The AFP coding sequence can be fused in-frameto the pre-pro-α-factor leader region. This construct can then be putunder the control of a strong transcriptional promoter, such as thealcohol dehydrogenase I promoter, actin, or a glycolytic promoter.Alternatively, inducible promoters can also be used, such as thosedependent on the presence or absence of metal ions (i.e., CUP1 promoter,also known as metallothionein promoter), glucose, galactose (i.e., GAL1,GAL10), or other sugars. The fusion protein coding sequence can befollowed by a translation termination codon, which can be followed bytranscription termination signals. Vectors useful for expression inyeast include, without limitation, the 2μ circle plasmid (Broach, J. R.et al, (1979) Gene 8(1): 121-33) and the centromeric plasmid (Hsiao, C.L. and Carbon, J. (1981) Proc. Natl. Acad. Sci. 78(6): 3760-4).

Efficient post-translational modification and expression of recombinantproteins can also be achieved in Baculovirus systems in insect cells(“Baculovirus Expression Protocols,” Humana Press Inc.; WO92/005264).These systems are well known in the art.

Mammalian cells are useful to express and purify the AFPs of theinvention, especially when the protein is purified for administration tomammalian subjects. Vectors useful for the expression of proteins inmammalian cells often have strong viral promoters to direct expressionand can also include other sequences that are useful for directingexpression in human cells, such as enhancers, polyadenylation signals,and other signal sequences for promoting transcription, translation,i.e., internal ribosomal entry sites (IRES) and/or the processing of theAFPs of the invention. In certain embodiments of the invention where theuse of IRES elements may be necessary, IRES elements may be derived fromviruses, such as the picornavirus family (polio andencephalomyocarditis) IRES and the hepatitis C virus IRES, or frommammalian mRNA such as the mammalian BiP IRES. Alternatively oradditionally, the plasmid in the DNA vaccine or immunogenic compositioncan further contain and express in a subject host cell a nucleotidesequence encoding a heterologous tPA signal sequence such as human tPAand/or a stabilizing intron, such as intron II of the rabbit β-globingene.

Depending on the vector, selectable markers encoding antibioticresistance may be present when used for in vitro purification, such as,but not limited to, ampicillin, tetracycline, neomycin, zeocin,kanamycin, bleomycin, hygromycin, chloramphenicol, among others.Selection systems that do not use antibiotic resistance genes can alsobe used in the expression vector and mammalian host system. Promotersequences that can be used to direct expression of the AFPs include, butare not limited to, strong viral promoters, such as the promoter fromhuman cytomegalovirus (CMV), the promoter from the thymidine kinase geneof herpes simplex virus (HSV), promoters from adenoviruses such as theAdenovirus 5E2 Collagenase promoter, β-actin promoter, Muscle CreatineKinase promoter and composite promoters such as the EF-1a/HTLV promoter(InVitrogen) and the ferritin composite promoters comprised of the FerHor FerL core promoters (InVitrogen) among others. Among preferredeukaryotic expression vectors are pWLNEO, pSV2CAT, pOG44, pXTI and pSGavailable from Stratagene; and pSVK3, pBPV, pMSG and pSVL available fromPharmacia. The AFP coding sequence can be introduced into a mammaliancell line capable of synthesizing intact proteins have been developed inthe art and include, but arc not limited to, CHO, COS, 293, 293T, HeLa,NIH 3T3, Jurkat, myeloma and PER.C6 cell lines. Presence of theexpression vector-derived RNA in the transfected cells can be confirmedby Northern blot analysis and production of a cDNA or opposite strandRNA corresponding to the protein coding sequence can be confirmed bySouthern and Northern blot analysis, respectively.

Cell transformation techniques and gene delivery methods (such as thosefor in vivo use to deliver genes) are well known in the art. Any suchtechnique can be used to deliver a nucleic acid or expression vectorencoding an AFP of the invention to a cell or subject, respectively.

The AFPs of the invention can be purified from bacterial, yeast, insector mammalian cells using techniques well-known in the art. For example,the AFPs can be purified or concentrated using ammonium sulfate orethanol precipitation, acid extraction, anion or cation exchangechromatography, phosphocellulose chromatography, hydrophobic interactionchromatography, affinity chromatography, immuno-affinity chromatography,hydroxyapatite chromatography, lectin chromatography, molecular sievechromatography, isoelectric focusing, gel electrophoresis, combinationsof these methods using monitoring techniques to follow the distributionof the AFP at each purification step as well as the purity of the AFP.Some or all of the foregoing purification steps, in various combinationsor with other known methods, can also be employed to providesubstantially purified, isolated AFPs of the invention. If the AFPcontains an epitope recognized by a monoclonal or polyclonal antibody,then immunoaffinity purification can be used alone or in conjunctionwith the above techniques. For immunoaffinity chromatography, the AFP(or a cellular extract or other mixture containing the AFP) can bepurified by passage through a column containing a resin, which has boundthereto antibodies specific for the antigenic peptide. Immunoaffinitypurification can also be conducted in batches when the affinity reagentis bound to a solid support. Such techniques are well known in the art.

IV. Immunogenic Compositions and Adjuvants

In yet another aspect, the invention provides an immunogenic compositioncomprising the AFPs, nucleic acids or expression vectors of theinvention in admixture with a pharmaceutically acceptable carrier. Suchcarriers are also acceptable for immunological use. The immunogeniccompositions of the invention are useful to stimulate an immune responseagainst HIV as one or more components of a prophylactic or therapeuticvaccine against HIV for the prevention, amelioration or treatment ofAIDS. The nucleic acids and vectors of the invention are particularlyuseful for providing genetic vaccines, i.e. vaccines for delivering thenucleic acids encoding the AFPs of the present invention to a subjectsuch as a human, such that the AFPS are then expressed in the subject toelicit an immune response.

The compositions of the invention may be injectable suspensions,solutions, sprays, syrups or elixirs. To prepare such a composition, anAFP, nucleic acid or expression vector of the invention, having thedesired degree of purity, is mixed with one or more pharmaceuticallyacceptable carriers and/or excipients. The carriers and excipients mustbe “acceptable” in the sense of being compatible with the otheringredients of the composition. Acceptable carriers, excipients, orstabilizers are nontoxic to recipients at the dosages and concentrationsemployed, and include, but are not limited to, water, saline, phosphatebuffered saline, dextrose, glycerol, ethanol, or combinations thereof,buffers such as phosphate, citrate, and other organic acids;antioxidants including ascorbic acid and methionine; preservatives (suchas octadecyldimethylbenzyl ammonium chloride; hexamethonium chloride;benzalkonium chloride, benzethonium chloride; phenol, butyl or benzylalcohol; alkyl parabens such as methyl or propyl paraben; catechol;resorcinol; cyclohexanol; 3-pentanol; and m-cresol); low molecularweight (less than about 10 residues) polypeptide; proteins, such asserum albumin, gelatin, or immunoglobulins; hydrophilic polymers such aspolyvinylpyrrolidone; amino acids such as glycine, glutamine,asparagine, histidine, arginine, or lysine; monosaccharides,disaccharides, and other carbohydrates including glucose, mannose, ordextrins; chelating agents such as EDTA; sugars such as sucrose,mannitol, trehalose or sorbitol; salt-forming counter-ions such assodium; metal complexes (e.g., Zn-protein complexes); and/or non-ionicsurfactants such as TWEEN™, PLURONICS™ or polyethylene glycol (PEG).

An immunogenic or immunological composition can also be formulated inthe form of an oil-in-water emulsion. The oil-in-water emulsion can bebased, for example, on light liquid paraffin oil (European Pharmacopeatype); isoprenoid oil such as squalane, squalene, EICOSANE™ ortetratetracontane; oil resulting from the oligomerization of alkene(s),e.g., isobutene or decene; esters of acids or of alcohols containing alinear alkyl group, such as plant oils, ethyl oleate, propylene glycoldi(caprylate/caprate), glyceryl tri(caprylate/caprate) or propyleneglycol dioleate; esters of branched fatty acids or alcohols, e.g.,isostearic acid esters. The oil advantageously is used in combinationwith emulsifiers to form the emulsion. The emulsifiers can be nonionicsurfactants, such as esters of sorbitan, mannidc (e.g., anhydromannitololeate), glycerol, polyglycerol, propylene glycol, and oleic,isostearic, ricinoleic, or hydroxystearic acid, which are optionallyethoxylated, and polyoxypropylene-polyoxyethylene copolymer blocks, suchas the Pluronic® products, e.g., L121. The adjuvant can be a mixture ofemulsifier(s), micelle-forming agent, and oil such as that which iscommercially available under the name Provax® (IDEC Pharmaceuticals, SanDiego, Calif.).

The immunogenic compositions of the invention can contain additionalsubstances, such as wetting or emulsifying agents, buffering agents, oradjuvants to enhance the effectiveness of the vaccines (Remington'sPharmaceutical Sciences, 18th edition, Mack Publishing Company, (ed.)1980).

Adjuvants include, but are not limited to mineral salts (e.g.,AlK(SO₄)₂, AlNa(SO₄)₂, AlNH(SO₄)₂, silica, alum, Al(OH)₃, Ca₃(PO₄)₂,kaolin, or carbon), polynucleotides with or without immune stimulatingcomplexes (ISCOMs) (e.g., CpG oligonucleotides, such as those describedin Chuang, T. H. et al, (2002) J. Leuk. Biol. 71(3): 538-44;Ahmad-Nejad, P. et al (2002) Eur. J. Immunol. 32(7): 1958-68; poly IC orpoly AU acids, polyarginine with or without CpG (also known in the artas IC31; see Schellack, C. et al (2003) Proceedings of the 34^(th)Annual Meeting of the German Society of Immunology; Lingnau, K. et al(2002) Vaccine 20(29-30): 3498-508), JuvaVax™ (U.S. Pat. No. 6,693,086),certain natural substances (e.g., wax D from Mycobacterium tuberculosis,substances found in Cornyebacterium parvum, Bordetella pertussis, ormembers of the genus Brucella), flagellin (Toll-like receptor 5 ligand;see McSorley, S. J. et al (2002) J. Immunol. 169(7): 3914-9), saponinssuch as QS21, QS17, and QS7 (U.S. Pat. Nos. 5,057,540; 5,650,398;6,524,584; 6,645,495), monophosphoryl lipid A, in particular,3-de-O-acylated monophosphoryl lipid A (3D-MPL), imiquimod (also knownin the art as IQM and commercially available as Aldara®; U.S. Pat. Nos.4,689,338; 5,238,944; Zubcr, A. K. et al (2004) 22(13-14): 1791-8), andthe CCR5 inhibitor CMPD167 (see Veazey, R. S. et al (2003) J. Exp. Med.198: 1551-1562).

Aluminum hydroxide or phosphate (alum) are commonly used at 0.05 to 0.1%solution in phosphate buffered saline. Other adjuvants that can be used,especially with DNA vaccines, are cholera toxin, especiallyCTA1-DD/ISCOMs (see Mowat, A. M. et al (2001) J. Immunol. 167(6):3398-405), polyphosphazenes (Allcock, H. R. (1998) App. OrganometallicChem. 12(10-11): 659-666; Payne, L. G. et al (1995) Pharm. Biotechnol.6: 473-93), cytokines such as, but not limited to, IL-2, TL-4, GM-CSF,IL-12, IGF-1, IFN-α, IFN-β, and IFN-γ (Boyer et al., (2002) J. LiposomeRes. 121:137-142; WO01/095919), immunoregulatory proteins such as CD40L(ADX40; see, for example, WO03/063899), and the CD1a ligand of naturalkiller cells (also known as CRONY or α-galactosyl ceramide; see Green,T. D. et al, (2003) J. Virol. 77(3): 2046-2055), immunostimulatoryfusion proteins such as TL-2 fused to the Fc fragment of immunoglobulins(Barouch et al., Science 290:486-492, 2000) and co-stimulatory moleculesB7.1 and B7.2 (Boyer), all of which can be administered either asproteins or in the form of DNA, on the same expression vectors as thoseencoding the AFP of the invention or on separate expression vectors.

Cytokines that may be used in the present invention include, but are notlimited to, granulocyte colony stimulating factor (G-CSF),granulocyte/macrophage colony stimulating factor (GM-CSF), interferon α(IFN α), interferon (β (IFN β), interferon γ, (IFN γ), interleukin-1α(IL-1 α), interleukin-1 β (IL-1 β), interleukin-2 (IL-2), interleukin-3(IL-3), interleukin-4 (IL-4), interleukin-5 (IL-5), interleukin-6(IL-6), interleukin-7 (IL-7), interleukin-8 (IL-8), interleukin-9(IL-9), interleukin-10 (IL-10), interleukin-11 (IL-11), interleukin-12(IL-12), tumor necrosis factor a (TNF α), tumor necrosis factor β (TNFβ), and transforming growth factor β (TGF β). It is understood thatcytokines can be co-administered and/or sequentially administered withthe immunogenic or vaccine composition of the present invention. Thus,for instance, a virus propagated in the instant invention can contain anexogenous nucleic acid molecule and express in vivo a suitable cytokine,e.g., a cytokine matched to this host to be vaccinated or in which animmunological response is to be elicited (for instance, an humancytokine for compositions to be administered to humans).

The immunogenic compositions can be designed to introduce the AFP,nucleic acid or expression vector to a desired site of action andrelease it at an appropriate and controllable rate. Methods of preparingcontrolled-release formulation are known in the art. For example,controlled release preparations can be produced by the use of polymersto complex or absorb the immunogen and/or immunogenic composition. Acontrolled-release formulations can be prepared using appropriatemacromolecules (for example, polyesters, polyamino acids, polyvinyl,pyrrolidone, ethylenevinylacetate, methylcellulose,carboxymethylcellulose, or protamine sulfate) known to provide thedesired controlled release characteristics or release profile. Anotherpossible method to control the duration of action by acontrolled-release preparation is to incorporate the active ingredientsinto particles of a polymeric material such as, for example, polyesters,polyamino acids, hydrogels, polylactic acid, polyglycolic acid,copolymers of these acids, or ethylene vinylacetate copolymers.Alternatively, instead of incorporating these active ingredients intopolymeric particles, it is possible to entrap these materials intomicrocapsules prepared, for example, by coacervation techniques or byinterfacial polymerization, for example, hydroxymcthylccllulosc orgelatin-microcapsule and poly-(methylmethacrylate) microcapsule,respectively, in colloidal drug delivery systems (for example,liposomes, albumin microspheres, microemulsions, nano-particles andnanocapsules) or in macroemulsions. Such techniques are disclosed in NewTrends and Developments in Vaccines, Voller et al. (eds.), UniversityPark Press, Baltimore, Md., 1978 and Remington's PharmaceuticalSciences, 16th edition.

Suitable dosages of the AFP, nucleic acids and expression vectors of theinvention (collectively, the immunogens) in the immunogenic compositionof the invention can be readily determined by those of skill in the art.For example, the dosage of the immunogens can vary depending on theroute of administration and the size of the subject. A suitable dose ofAFP of the invention can range from about 1-10 μg to about 5000 mg, andis typically from about 500 μg to about 100 mg, depending inter alia onthe molecular weight of the AFP, the route of delivery, the deliverymeans and the body mass of the recipient. A suitable dose of nucleicacid of the invention can range from about 1 μg to about 100 mg, andmore typically from about 10-100 μg to about 1-10 mg again depending,inter alia, on the factors assessed for protein delivery, as well as thesize of the nucleic acid molecule. The dosages for delivery ofexpression vectors of the invention depends additionally on the natureof the expression vector. When the vector is an RNA or DNA molecule(including plasmids or a plasmid incorporated in a lipid or otherdelivery particle), then the amount of expression vector in a dosage issimilar to that of the nucleic acids of the invention. The dosage forbacterial expression vectors is conveniently characterized according tocolony forming units (cfu). The dose will preferably range from about10⁴ to about 10¹⁰ cfu and more preferably from about 10⁶ to about 10¹⁰cfu, as well as from about 10⁸ to about 10⁹ cfu. The dosage for viralexpression vectors depends on the nature of the vector, e.g., whetherthe vector is an alphavirus, an adenovirus, AAV, a poxvirus, aretrovirus and the like. Any of these doses can be calculated on a unitdosage basis or as an amount per kilogram body weight of the subject.

Doses for administering viral vectors are well known and can bedetermined by those of skill in the art if needed. By way of example,when the agent is a viral vector, such as a replication-defectiveadenovirus, the dosage can range from about 10⁶ to about 10¹² plaqueforming units (pfu), and is preferably between about 10⁸ to about 10¹⁰pfu. For stable and efficient transduction using a recombinant AAV, thedosage can be from about 1×10⁵ IU (infectious units) of AAV per grambody weight to about 1×10⁹ IU AAV per gram body weight, and preferablyfrom about 1×10⁶ IU AAV per gram body weight to about 1×10⁷ IU AAV pergram body weight. For poxviruses and MVA, dosages ranging from about 10⁵to about 10¹⁰ pfu, are useful; dosages of about 10⁷ to about 10⁸ pfu areoften used.

Other suitable doses can be determined by those of skill in the art. Todetermine appropriate doses, those of skill in the art can measure theimmune response of subjects by conventional immunological techniques andadjust the dosages as appropriate. Such techniques include but are notlimited to, e.g., chromium release assay, tetramer binding assays, IFN-γELISPOT assays and intracellular cytokine assays as well as otherimmunological detection assays, e.g., as detailed in Harlow.

The present invention provides methods for expressing an AFP of theinvention in animal cells by introducing an expression vector of theinvention into the animal cells and culturing those cells underconditions sufficient to express the AFP. The expression vector can beintroduced by any appropriate method including, but not limited to,transfection, transformation, microinjection, infection,electroporation, particle bombardment and the like. Such techniques arestandard in the art. After introducing the expression vector, the cellsare maintained under the appropriate culture conditions (i.e., for atime and at the appropriate conditions) to maintain cell viability atleast until the AFP is expressed. In some instances, for example withalphavirus replicon vectors, expression of the AFP includes productionof an RNA molecule encoding the AFP.

In addition, the invention provides methods for introducing andexpressing an AFP of the invention in an animal by delivering anexpression vector of the invention in to the animal and therebyobtaining expression of the AFP in the animal. Any delivery method canbe used including parenteral, subcutaneous, epicutaneous, oral, peroral,intramuscular, intravenous, intradermal, intranasal, mucosal, topical orother delivery method, such as the particle bombardment method byPowderject (a needle-less delivery system to the skin that is actuatedby helium gas). Such techniques are well known to those of skill in theart. The expression vectors can be formulated as needed to improvestability and delivery efficiency. Once the expression vector isdelivered, the ORF of the AFP is transcribed (if needed) and translatedto express the encoded AFP. One of skill in the art is familiar withmethods of in vitro and in vivo transcription and translation.

Such methods for expressing AFPs in animal cells and in animals areuseful, for example, as clinical, diagnostic, or other research toolsfor studying the mechanisms of AFP expression, localization of AFPs,mechanisms of signal transduction pathways affected or induced inresponse to AFP expression, and the effects of various nucleic acidcontrol elements on AFP expression and localization.

In accordance with the invention, the AFPs, nucleic acids and expressionvectors of the invention can serve as immunogens for inducing immuneresponses in animals, particularly HIV specific CTL immune responses.Hence as used herein, the immunogen is the molecule that is delivered tothe animal and that directly or indirectly leads to production of animmune response (either humoral or cellular). An HIV immunogen induces aresponse against HIV which response can be cellular or humoral. HIVCON,RENTA, and HIVA are examples of HIV protein immunogens (see WO 01/47955for HIVA; PCT/US2004/037699 for RENTA). pTHr.HIVCON, pTHr.RENTA, andpTHr.HIVA are examples of DNA- or plasmid-vectored HIV immunogens.MVA.HIVCON, MVA.RENTA, and MVA.HIVA are examples of virally-vectored HIVimmunogens.

The present methods are useful as research tools when immunizinglaboratory animals to study the immune response to these immunogenseither alone or in conjunction with other HIV immunogens, as well aswith or without adjuvants. More particularly, the methods can be forprophylactic or therapeutic prevention, amelioration or treatment of HIVin humans. When provided prophylactically, the methods are ideallyadministered to a subject in advance of any evidence of HIV infection orin advance of any symptom due to AIDS, especially in high-risk subjects.The prophylactic administration of the immunogens can serve to preventor attenuate AIDS in a human subject. When provided therapeutically, themethods can serve to ameliorate and treat AIDS symptoms and areadvantageously used as soon after infection as possible, preferablybefore appearance of any symptoms of AIDS but may also be used at (orafter) the onset of the disease symptoms.

The recombinant vectors express a nucleic acid molecule encoding AFPs ofthe present invention. In particular, the AFPs can be isolated,characterized and inserted into vector recombinants. The resultingrecombinant vector is used to immunize or inoculate a subject.Expression in the subject of the AFPs can result in an immune responsein the subject to the expression products of the AFP. Thus, therecombinant vectors of the present invention may be used in animmunological composition or vaccine to provide a means to induce animmune response, which may, but need not be, protective.

To induce or stimulate an immune response, an AFP or an expressionvector of the invention or AFP of the invention is delivered one or moretimes into the subject so that the encoded AFP is expressed at a levelsufficient to induce an immune response to the AFP, or the AFP isprovided in an amount sufficient to induce an immune response to AFP.Any delivery method can be used including, but not limited to,intramuscular, intravenous, intradermal, mucosal, and topical delivery.Such techniques are well known to those of skill in the art. Morespecific examples of delivery methods are intramuscular injection,intradermal injection, and subcutaneous injection. However, deliveryneed not be limited to injection methods. Further, delivery of DNA toanimal tissue has been achieved by cationic liposomes (Watanabe et al.,(1994) Mol. Reprod. Dev. 38:268-274; and WO 96/20013), direct injectionof naked DNA into animal muscle tissue (Robinson et al., (1993) Vaccine11:957-960; Hoffman et al., (1994) Vaccine 12: 1529-1533; Xiang et al.,(1994) Virology 199: 132-140; Webster et al., (1994) Vaccine 12:1495-1498; Davis et al., (1994) Vaccine 12: 1503-1509; and Davis et al.,(1993) Hum. Mol. Gen. 2: 1847-1851), or intradermal injection of DNAusing “gene gun” technology (Johnston et al., (1994) Meth. Cell Biol.43:353-365). Alternatively, delivery routes (especially for bacterialexpression vectors, e.g., attenuated Salmonella or Shigella spp.) can beoral, intranasal or by any other suitable route. Delivery also beaccomplished via a mucosal surface such as the anal, vaginal or oralmucosa.

Immunization schedules (or regimens) are well known for animals(including humans) and can be readily determined for the particularsubject and immunogen (whether an AFP or an expression vector). Hence,the immunogens can be administered one or more times to the subject.Preferably, there is a set time interval between administration of theimmunogen. While this interval varies for every subject, typically itranges from 10 days to several weeks, and is often 2, 4, 6 or 8 weeks.For humans, the interval is typically from 2 to 6 weeks. Theimmunization regimes typically have from 1 to 6 administrations ofimmunogen, but may have as few as one or two or four. The methods ofinducing an immune response can also include administration of anadjuvant with the immunogens. In some instances, annual, biannual orother long interval (5-10 years) booster immunization can supplement theinitial immunization protocol.

The present methods include a variety of prime-boost regimens,especially DNA prime-MVA boost regimens. In these methods, one or morepriming immunizations are followed by one or more boostingimmunizations. The actual antigen can be the same or different for eachimmunization and the type of immunogen (e.g., protein or expressionvector), the route, and formulation of the immunogens can also bevaried. For example, if an expression vector is used for the priming andboosting steps, it can either be of the same or different type (e.g.,DNA or bacterial or viral expression vector). One useful prime-boostregimen provides for two priming immunizations, four weeks apart,followed by two boosting immunizations at 4 and 8 weeks after the lastpriming immunization. It should also be readily apparent to one of skillin the art that there are several permutations and combinations that areencompassed using the DNA, bacterial and viral expression vectors of theinvention to provide priming and boosting regimens.

A specific embodiment of the invention provides methods of inducing animmune response against HIV in a human by administering an AFP of theinvention, a nucleic acid of the invention and/or an expression vectorof the invention one or more times to a subject wherein the AFP isadministered in an amount or expressed at a level sufficient to inducean HIV-specific CTL immune response in the subject. Such immunizationscan be repeated multiple times at time intervals of at least 2, 4 or 6weeks (or more) in accordance with a desired immunization regime.

The method can be used in combination with, including proteins orexpression vectors that encode such other antigens. The compositions canbe administered alone, or can be co-administered or sequentiallyadministered with other HIV immunogens and/or HIV immunogeniccompositions, e.g., with “other” immunological, antigenic or vaccine ortherapeutic compositions thereby providing multivalent or “cocktail” orcombination compositions of the invention and methods of employing them.Again, the ingredients and manner (sequential or co-administration) ofadministration, as well as dosages can be determined taking intoconsideration such factors as the age, sex, weight, species andcondition of the particular subject, and the route of administration.

When used in combination, the other HIV immunogens can be administeredat the same time or at different times as part of an overallimmunization regime, e.g., as part of a prime-boost regimen or otherimmunization protocol. Many other HIV immunogens are known in the art,one such preferred immunogen is HIVA (described in WO 01/47955), whichcan be administered as a protein, on a plasmid (e.g., pTHr.HIVA) or in aviral vector (e.g., MVA.HIVA). Another such HIV immunogen is RENTA(described in PCT/US2004/037699), which can also be administered as aprotein, on a plasmid (e.g., pTHr.RENTA) or in a viral vector (e.g.,MVA.RENTA).

For example, one method of inducing an immune response against HIV in ahuman subject comprises administering at least one priming dose of anHIV immunogen and at least one boosting dose of an HIV immunogen,wherein the immunogen in each dose can be the same or different,provided that at least one of the immunogens is an AFP of the invention,a nucleic acid encoding an AFP of the invention or an expression vectorencoding an AFP of the invention, and wherein the immunogens areadministered in an amount or expressed at a level sufficient to inducean HIV-specific immune response in the subject. The HIV-specific immuneresponse can include an HIV-specific CTL immune response. Suchimmunizations can be done at intervals, preferably of at least 2-6weeks.

In accordance with this method, pTHr.HIVCON is administered one or moretimes as the priming dose or MVA.HIVCON is administered one or moretimes as the boosting dose, with or without the priming dose having beenpTHr.HIVCON. As an example of using another HIV immunogen in thismethod, the priming dose can be pTHr.HIVCON and the boosting dose can beMVA.HIVCON, MVA.RENTA, MVA.HIVA, or a mixture of MVA.HIVCON, MVA.RENTAand MVA.HIVA, and combinations thereof. When mixtures are used in thepriming or boosting doses, the components can be mixed together foradministration or administered separately. When administered separately,the components can be also be administered sequentially as multipleseparate priming or boosting doses administered at an interval of 2-6weeks from each other. One example of an immunization regimen of thismethod is to administer two priming doses at weeks 0 and 4, each dosebeing a mixture of pTHr.HIVCON and pTHr.RENTA or pTHr.HIVA, followed byadministration of two boosting doses at weeks 8 and 12, each dose beinga mixture of MVA.HIVCON, MVA.RENTA, and MVA.HIVA.

The immune response induced by the methods of the invention can beassessed by standard techniques known in the art. For CTL responses,such techniques include but are not limited to, intracellular IFN-γstaining assays, tetramer assays, ELISPOT assays (Beattie, T. et al(2004) AIDS 18(11): 1595-8), and ⁵¹Cr-release assays. A systematiccomparison of CTL detection methods can be found in Sun, Y. et al (2003)J. Immunol. Meth. 272(1-2): 23-34; and in Shacklett, B. L. (2002) J.Clin. Immunol. 130(2): 172-82. Other immune responses can be assessed asdescribed in Harlow.

The present invention also comprehends compositions and methods formaking and using vectors, including methods for producing gene productsand/or immunological products and/or antibodies in vivo and/or in vitroand/or ex vivo (e.g., the latter two being, for instance, afterisolation therefrom from cells from a host that has had anadministration according to the invention, e.g., after optionalexpansion of such cells), and uses for such gene and/or immunologicalproducts and/or antibodies, especially neutralizing antibodies to HIV(reviewed in Haigwood, N. L. and Stamatatos, L. (2003) 17 (Suppl 4:S67-71), including in diagnostics (reviewed in Truong, H. M. andKlausner, J. D. (2004) MLO Med Lab Obs. 36(7): 12-13, 16, 18-20),assays, therapies, treatments, and the like. The resulting neutralizingantibodies can be used separately, or in combination with the AFPs ofthe present invention to enhance or modulate immunogenic orimmunological responses to HIV, SIV, or STV/HIV hybrids. Theneutralizing antibodies can be tailored for specificity to a particularClade or CRF, or can be clade-universal. The AFPs of the presentinvention can be used, in particular, in developing neutralizingantibodies directed to a specific HIV protein sequence that arecross-clade or clade-universal.

The invention also includes the use of the vectors expressing AFPs inthe research setting. The vectors can be used to transfect or infectcells or cell lines of interest to study, for example, cellularresponses to gene products expressed from the heterologous sequences ofinterest, or signal transduction pathways mediated by proteins encodedby the heterologous sequences of interest. Such signal transductionpathways can include cytokine expression, or up- or downregulation ofgenes, such as but not limited to cellular receptors or cell-surfacemarker proteins, i.e., CD4, CCR5, CXCR5, MHC Class I and II, in responseto expression of HIV proteins.

In the research setting, it is often advantageous to design recombinantvectors or viruses that comprise reporter genes that can be easilydetected by laboratory assays and techniques. Reporter genes are wellknown in the art and can comprise resistance genes to antibiotics suchas, but not limited to, ampicillin, tetracycline, neomycin, zeocin,kanamycin, bleomycin, hygromycin, chloramphenicol, among others.Reporter genes can also comprise green fluorescent protein, the lacZgene (which encodes β-galactosidase), luciferase, and β-glucuronidase.

The invention further relates to the product of expression of the AFPand uses thereof, such as to produce a protein in vitro, or to formantigenic, immunological or vaccine compositions for treatment,prevention, diagnosis or testing; and, to DNA from the recombinantvectors, which are useful in constructing DNA probes, antisense RNAmolecules, small interfering RNA molecules (siRNA), ribozymes, and PCRprimers. The invention also comprehends producing synthetic peptidesusing the AFPs described herein (see above). The invention can encompassuse of the AFPs to identify new or existing isolates, Clades, and CRFsof HIV arising in the environment, i.e. in the circulating population orgeographic region, or in a single individual (Ito, Y. et al (2003) J.Clin. Microbiol. 41(5): 2126-31). The AFPs of the invention can also beused, for example, to determine specificity of responses, or mechanismsof resistance, to currently available anti-HIV drugs and therapies incells or subjects infected with HIV. The efficacy of anti-HIV drugs isoften dependent on the Clade or CRF of HIV present in the subject orpopulation of subjects; thus a cross-clade or clade-universal AFP of thepresent invention can be used advantageously to develop new or optimizedanti-HIV drugs or therapies that can be applied to all HIV Clades orCRFs. Additionally, the efficacy of currently available anti-HIV drugsand therapies, such as, for example, AZT, protease inhibitors, fusioninhibitors, and combination therapies thereof, among others, can bemodulated or optimized by, inter alia, administering the drug or therapyto cells or subjects expressing the AFP.

The AFPs of the present invention can be used separately, orconcurrently with existing anti-HIV therapies, including drug regimensor therapies such as HAART (highly active anti-retroviral therapy),neutralizing antibodies, but are not limited to these examples.

The AFPs of the present invention can also be altered or modified toinclude sequences from SIV, or from SIV/HIV hybrids, to produce antherapeutic or prophylactic immunogenic or immunological response innon-human primates. The AFPs of the invention can be modified forinclusion in non-human animal models of HIV. One of the skill in the artcan easily modify the AFPs of the present invention to encompass SIVsequences and CTL epitopes to induce an immune response that may, butneed not be, protective.

It is to be understood and expected that variations in the principles ofinvention herein disclosed in exemplary embodiments may be made by oneskilled in the art and it is intended that such modifications, changes,and substitutions are to be included within the scope of the presentinvention. All of the patents and publications cited herein are herebyincorporated by reference.

The following examples are given for the purpose of illustrating variousembodiments of the invention and are not meant to limit the presentinvention in any fashion.

EXAMPLES Example 1 HIVCON Plasmid Construction

The HIVCON ORF (see SEQ ID NO: 1, FIG. 2, and SEQ ID NO: 5, FIG. 6) wasdesigned to encode a chimeric protein derived from the highly conserveddomains of HIV proteins. HIVCON chimeric protein contains the 14 mostconserved protein domains of HIV with the domains having less than 6%variability between four major HIV Clades A-D. The HIVCON ORF iscontained within the HIVCON gene fragment, which also can include theMamu-A*01 (SIV Gag p27) epitope, the murine P18-I10 (H-2^(K)) epitopeand the mAb epitope Pk. The HIVCON gene fragment was synthesized(geneART GmbH, Germany) using preferred human amino acid codon usage(Andre, S. et al (1998) J. Virol. 72(2): 1497-1503). The HIVCON ORF ispreceded by a 12-nucleotide consensus Kozak sequence (Kozak, (1987)Nucleic Acid Res. 15:8125-8148) (see SEQ ID NO: 5, FIG. 6). Thenucleotide sequences encoding the 14 conserved HIV protein domains weredirectly fused to each other with the Mamu-A*01 epitope, P18-I10epitope, presented by H-2^(K) (Romero et al), and the mAb epitope Pkfused to the C-terminal conserved protein fragment, thus creating theHIVCON coding sequence of SEQ ID NO. 3 (FIG. 4). The entire syntheticgene fragment was sequenced to verify the accuracy of gene synthesis.When a synthesis error was detected, the improper nucleotide(s) wasreplaced with the correct nucleotide using site-directed mutagenesis.The HIVCON gene fragement was inserted into plasmid pTH (Hanke 1998a) togenerate the pTH expression vector. All recombinant DNA manipulationswere performed using standard procedures (Sambrook et al., MolecularCloning; A Laboratory Manual (2nd ed.), Cold Spring Harbor Press, ColdSpring Harbor, N.Y. 1989).

In the experiments presented herein, the pTH.HIVCON vector was used.However, it should be noted that for use in human patients, it ispreferred that the β-lactamase gene (ampicillin resistance gene) frompTH is removed (for example by excising the plasmid at the BspHI sitesand religating the linear fragment containing HIVCON) to generate thepTHr.HIVCON expression vector. The pTHr.HIVCON plasmid uses anauxotrophic repressor-titration system for bacterial selection and doesnot carry any antibiotic-resistance gene (Williams et al., (1998)Nucleic Acid Res. 26:2120-2124; U.S. Pat. No. 5,972,708). In the pTHrvector, HIVCON transcription is controlled by an efficientenhancer/promoter/intron A cassette derived from the humancytomegalovirus strain AD 169 (Whittle et al., (1987) Protein Eng. 1:499-505) and a bovine polyadenylation site (Goodwin et al., (1992) J.Biol. Chem. 267: 16330-16334). Such a pTHr.HIVCON vector will beparticularly useful as a vector for use in humans, i.e. for GMP clinicalvaccines.

HIVCONΔH is a version of the HIVCON gene in which the immunodominantmouse P18-I10 epitope of HIVCON gene (the coding sequence for which ispresent in SEQ ID NOs: 3, and the amino acids for which are those ofnucleotide positions 789-798 of SEQ ID NO:4) was deleted by PCR. Similarto HIVCON, HIVCONΔH was inserted in the pTH plasmid thus resulting inthe pTH. HIVCONΔH expression vector.

Example 2 Preparation of MVA.HIVCON and MVA.HIVCONΔH

The HIVCON fragment is excised out of pTHr.HIVCON using XmaI and ligatedinto the XmaI site of transfer vector pSC11 (Chakrabarti) to produce thevector pSC11.HIVCON used in the preparation of recombinant MVA.HIVCON.The plasmid pSC11.HIVCON carries the β-galactosidase gene.

The HIVCONΔH fragment fragment is cut out of pTHr.HIVCONΔH using XmaIand ligated into the XmaI site of transfer vector pSC11 (Chakrabarti) toproduce the vector pSC11.HIVCONΔH used in the preparation of recombinantMVA.HIVCONΔH. The plasmid pSC11.HIVCONΔH carries the β-galactosidasegene.

The HIVCON- or HIVCONΔH-coding fragment is inserted into the thymidinekinase locus of the virus genome under the p7.5 early/late vacciniapromoter using plasmid pSC 11, which co-delivers a β-galactosidase geneto facilitate screening, titration and stability studies of therecombinant MVA.HIVCON or MVA.HIVCONΔH (Chakrabarti). This marker enzymeis commonly expressed by human enteric bacteria and has been shown to besafe in several clinical trials, including healthy HIV-uninfectedvolunteers vaccinated with MVA.HIVA.

Briefly, recombinant MVA.HIVCON or MVA.HIVCONΔH virions are producedfrom chicken embryonic fibroblasts (CEF) cells grown in Dulbeco'sModified Eagle's Medium (DMEM) supplemented with 10% fetal calf serum(FCS), penicillin/streptomycin and glutamine (DMEM 10) that are infectedwith parental MVA at a multiplicity of infection (MOI) of 1 andtransfected using Superfectin (Qiagen, Germany) with 3 μg ofendotoxin-free pSC11.HIVCON. Recombinants are identified by a blue colorreaction of β-galactosidase in the presence of X-gal(5-bromo-4-chloro-3-indolyl-bD-galactoside). Recombinants are subjectedto five rounds of plaque purification, after which a master virus stockis grown, purified on a 36% sucrose cushion, titered and stored at −80°C. until use. The presence of the correct ORF, either HIVCON orHIVCONΔH, is confirmed by sequencing and immunofluorescence detection ofthe protein in MVA.HIVCON- or MVA.HIVCONΔH-infected cells.

Example 3 HIVCON and HIVCONΔH Expression in Human Cells

HIVCON and HIVCONΔH expression was assessed in human 293T cells or HEK293 cells transiently transfected with pTH.HIVCON or pTH.HIVCONΔH.HIVCON and HIVCOΔdH expression was assessed in human 293T cell infectedwith MVA.HIVCON or MVA.HIVCONΔH at an MOI of 5.

For immunofluorescence studies, six-well plates containing sterileslides pre-treated with poly-L-lysine (70,000-150,000 molecular mass;Sigma) were seeded with 293T cells (2×10⁵ cells per slide). Twenty fourhours later, the cell monolayers were transfected with either pTH.HIVCONor pTH.HIVCONΔH. To monitor the expression from the MVA constructs, thecell monolayers are infected with MVA.HIVCON or MVA.HIVCONΔH at an MOIof 5. After a 24-hour incubation at 37° C. with 5% CO₂, the cells werewashed and their membranes were perforated. The slides were blocked with2% FCS in phosphate-buffered saline (PBS) at 4° C. for 1 hour andincubated with a 1:200 dilution of the designated primary mAb at 4° C.overnight. The mAbs were against the Pk tag (Serotec, Oxford, UK). Afterincubation, the slides were washed once in PBS and incubated at 4° C.overnight with a 1:500 dilution of an Alexa Fluor® 594-conjugatedanti-mouse secondary antibody (Molecular Probes, Oregon, USA). Theslides were again washed once with PBS, stained with DAPI (4,6-diamidino-2-phenylindole 2HCl) nuclear stain (in Vectashield® mountingmedium, Vector Laboratories, USA) and photographed on a Zeissimmunofluoreseence microscope at 40× magnification.

The immunofluorescence results demonstrate that HIVCON and HIVCONΔHexpression is detectable in human cells using mAbs against the Pkepitope. FIG. 7 demonstrates the expression of HIVCON and HIVCONΔH in293T cells. The expression of the HIVCON protein from pTH.HIVCON plasmidDNA (A), pTH.HIVCONΔH plasmid DNA (B), MVA.HIVCON (C), MVA.HIVCONΔH (D)and Ad.HIVCON (E) in human 293T (A, B, C and D) or HEK 293 (E) cells wasdetected using immunofluorescence and mAb to the Pk tag of HIVCON. Thenuclei are shown in blue (appears as pale gray in black & white), Pk ingreen (appears as bright/white in black and white) (A, B, C and D) orred (appears as bright/white in black and white) (E).

Example 4 Genetic Stability of MVA.HIVCON and MVA.HIVCONΔH

The genetic stability of the inserted HIVCON or HIVCONΔH ORFs and β-galgenes is confirmed by seven blind sequential passages of the MVA.HIVCONand MVA.HIVCONdH in CEF cells. The original (passage 0) and the final(passage 7) virus stocks are then used to infect duplicate wells, ofwhich one well is stained with neutral red to detect any MVA plaques(both empty MVA and MVA.HIVCON or MVA.HIVCONdH) and the other well isstained with 5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside (X-gal) todetect the inserted β-gal gene (MVA.HIVCON or MVA.HIVCONdH)respectively. Comparison of the two titers suggests that MVA.HIVCON andMVA.HIVCONdH are stable above the sensitivity of this assay.Immunofluorescence analysis of CEF cells infected with viral stocks frompassages 0 and 7 indicates that the expression levels of HIVCON orHIVCONdH are comparable.

Example 5 Construction of Recombinant huAd5-GFP.HIVCON Vector

The HIVCON vaccine gene is inserted into Ad5 using the pAdEasy1adenoviral vector system (Hermeking, H. (1997) Mol. Cell 1: 3-11; He, T.C. et al (1998) Proc. Natl. Acad. Sci. 95(5): 2509-14). This systememploys efficient homologous recombination machinery in E. coli BJ5183bacterial cells (Nakamura, N. et al (2000) Mol. Cell Biol. 20(23):8969-8982), generating recombinant adenovirus genome by adouble-recombination event between the co-transformed adenoviralbackbone plasmid vector, pAdEasy1, and a shuttle vector pAd-TrackCMV,which carries the gene of interest. Viral production is convenientlyfollowed with the aid of green fluorescent protein (GFP), encoded by agene incorporated into the viral backbone. This system thus allows forthe generation of homogenous viruses without the risk of emptyadenovirus contamination.

Several PmeI-linearized, recombinant adenovirus DNA carrying the GFP andHIVCON genes are used to transfect six-well plates of HEK293 cells at70-80% confluency. At 8 days post-transfection, wells are scraped,centrifuged, and re-suspended in 2 ml Hanks Balanced Salt Solution(HBSS; Sigma). The cells are then subjected to four freeze/thaw cyclesin a dry ice/methanol bath and 50% of each viral supernatant are used tore-infect 50-70% confluent T-25 flasks of HEK293 cells. Two to 3 daysafter re-infection, virus is again harvested in a similar fashion andused to infect T-75 flasks and subsequently, T-175 flasks. This isrepeated for several rounds over a 10-day period prior to purification.

Purification of AdGFP-HIVCON is performed using the Adenopurelpurification kit (Puresyn Inc.; USA) as per manufacturer's instruction.In brief, four T-175 cm² flasks infected with AdGFP-HIVCON are scraped,subjected to 3 freeze/thaw cycles in a dry ice/methanol bath and thesupernatant obtained after pelleting of the cellular debris is passedover an absorber membrane with proprietary buffer formulations toisolate highly purified adenovirus preparations. Viral titer isdetermined by serial dilution of purified AdGFP-HIVCON in six-wellplates seeded with HEK293 cells at 70-80% confluence and enumeration ofGFP expressing cells 24-hours post-infection.

Example 6 HIVCON Immunogenicity in Mice

The immunogenicity of the pTH.HIVCON was assessed in mice using theP18-I10 epitope. Two groups of 5-6 week-old female BALB/c mice wereinjected into the anterior tibial muscles with 50 μg of endotoxin-freepTH.HIVCON in PBS under general anesthesia. Ten days later, the animalswere sacrificed and their spleens were removed. Individual spleens wereprocessed through a cell strainer (Falcon) using a 2-ml syringe rubberplunger. The splenocytes from each animal were washed twice andsuspended in 10 ml of lymphocyte medium (RPMI 1640 supplemented with 10%FCS penicillin/streptomycin, 20 mM HEPES and 15 mM 2-mercaptoethanol).Eight ml of splenocyte suspension was used for a bulk CTL culture.

To prepare the bulk CTL cultures, 8 ml of the splenocyte suspension wereincubated with 2 pg/ml of P18-I10 peptide in an humidified incubator in5% CO₂ at 37° C. for 5 days. On the day of the CTL assay, the cells werewashed 3 times with RPMI and resuspended at 10⁷ cells per ml in R10(RPMI 1640 supplemented with 10% FCS and penicillin/streptomycin) foruse as effector cells in a ⁵¹Cr-release assay.

For each batch of splenocytes, the effector cells were diluted 2-fold inU-bottom wells of a 96-well plate (Costar) using R10 medium to yieldeffector to target ratios between 200:1 to 3:1 after addition of thetarget cells. Five thousand ⁵¹Cr-labeled P815 target cells in R10 mediumwith or without 2 pg/ml of P18-I10 peptide were added to the effectorsand the mixture was incubated at 37° C. for 5 hours. Spontaneous andtotal chromium releases were estimated from wells containing targetcells in medium alone or in medium with 5% Triton X-100, respectively.The percentage specific lysis was calculated as [(samplerelease-spontaneous release)/(total release-spontaneous release)]×100.The spontaneous release was lower than 5% of the total counts perminute.

In FIG. 8, the left panel shows the results for mice immunized withpTHr.HIVA as control and the right panel shows the results for miceimmunized pTHr.HIVCON in the ⁵¹Cr-release assay with peptide-pulsed(solid circle) or unpulsed (open circle) target cells. All animalsresponded to the immunization and relatively high levels of lyticactivities were detected.

Example 7 Demonstration of Murine T-cell Responses to the HIVCONImmunogen

The T-cell response induced against the HIVCON immunogen was examinedwhen pTH.HIVCON was administered in BALB/c mice. Induction of specificimmune responses to the P18-I10 epitope of HIVCON was demonstrated usingan ex vivo intracellular cytokine staining assay. For this assay, mousesplenocytes isolated from mice treated with HIVA or HIVCON werestimulated with the appropriate P18-I10 peptide-pulsed P815 cells in thepresence of anti-CD28/anti-CD49d mAbs for 90 minutes at 37° C. in 5%CO₂. Brefeldin A was then added to inhibit cytokine secretion and thesamples were incubated for additional 6 hours before terminating thereaction with EDTA and FACS fix solution. The cells were permeabilizedand incubated with phycoerythrin (PE)-conjugated anti-CD8 andfluorescein isothiocyanate (FITC)-conjugated anti-IFN-γ mAbs (BDPharMingen) and analyzed using FACS.

The results in FIG. 9 demonstrate the CTL response induced by HIVCONimmunogen. The percentage of CD8+ splenocytes producing IFN-γ are shownfor mouse splenocytes isolated from mice treated with HIVA or HIVCONimmunogen and stimulated with P18-I10 peptide. The results furtherdemonstrate that the percentage of IFN-γ-producing CD8+ cells induced bythe HIVCON immunogen is approximately two-fold higher in animalsimmunized with pTH.HIVCON compared to animals immunized with the controlimmunogen HIVA. The percentage of CD8+ cells in the ConA column of thegraph serve as a positive control for CTL induction.

Example 8 Demonstration of Broad Murine T-cell Responses to HIVCON

The breadth of the T-cell responses induced against the HIVCON orHIVCONΔH immunogens is examined when either HIVCON, in the form ofpTH.HIVCON, pTHr.HTVCON, MVA.HIVCON or huAd5-GFP.HIVCON, or HIVCONΔH inthe form of pTH.HIVCONΔH, pTHr.HIVCONΔH or MVA.HIVCONdAH is administeredin BALB/c mice. Induction of specific immune response to the P18-I10epitope or specific epitopes of HIVCON is demonstrated using an ex vivointracellular cytokine staining assay. For this assay, mouse splenocytesare isolated from mice treated with HIVCON or HIVCONdH and aresubsequently stimulated with the appropriate P18-I10 peptide- or peptidepools pulsed P815 cells in the presence of anti-CD28/anti-CD49d mAbs for90 minutes at 37° C. in 5% CO₂. Brefeldin A is then added to inhibitcytokine secretion and the samples are incubated for additional 6 hoursbefore terminating the reaction with EDTA and FACS fix solution. Thecells are permeabilized and incubated with PE-conjugated anti-CD8 andFITC-conjugated anti-IFN-γ mAbs (BD PharMingen) and analyzed using FACS.

The results demonstrate that multiple specificities of CTL are inducedby the immunogens, where the percentage of CD8+ splenocytes producingIFN-γ from HIVCON or HIVCONdH immunized mice is significantly higherthan the percentage of CD8+ splenocytes producing IFN-γ from naive(unimmunized) mice.

The peptide pools consist of 15-mer peptides overlapping by 11 aminoacids across the entire length of the HIVCON immunogen. Each pool caninclude peptides that cover approximately 50-100 amino acids from thelength of the HIVCON immunogen.

Example 9 In Vitro CFSE Proliferation Assay

A carboxy-fluorescein diacetate succinimidyl ester (CFSE) staining assaywas used to monitor the proliferative capacity of splenocytes from miceimmunized with pTH.HIVA or pTH.HIVCON and restimulated with the P18-I10peptide. BALB/c mice were immunized with a single shot of 100 μg DNAintramuscularly. Splenocytes were harvested after ten days and isolatedsplenocytes were stained with CFSE (Molecular Probes) at a finalconcentration of 2 μM at 37° C. for 10 min. The reaction was stopped bythe addition of fetal calf serum. Cells were washed three times,resuspended in lymphocyte medium and restimulated with 2 μg/ml P18-I10peptide. Splenocytes cultures were incubated at 37° C., 5% CO₂ for 5days, analyzed on a FACScan (BD) and data analysis was performed usingthe CellQuest software (BD). The results presented in FIG. 10demonstrate that the splenocytes from mice immunized with pTH.HIVCONcontinue to proliferate for multiple generations in culture, similar tosplenocytes restimulated with pTH.HIVA or ConA (positive controls), andin contrast to splenocytes that were not restimulated with P18-I10(negative control panel).

Example 10 Immunogenicity of HIVCON in Transgenic HHD Mice ExpressingHuman HLA

Transgenic HHD mice expressing interspecies HLA-A2 monochains have beendescribed previously (Pascolo et al. (1997) J Exp Med 185:2043-2051).These mice constitute a versatile murine model for the study of HLA-A2.1restricted CTL responses of potential human vaccines. The HHD transgenicanimals express the interspecies recombinant transgenic molecule,N-terminus human β2 m-HLA-A2.1 (α1α2)-mouse H-2D^(b)(α3), transmembrane,and cytoplasmic domains C-terminus, in the double knockout backgroundH-2D^(b−/−)β2 m^(−/−). Two approaches are undertaken to identify novelHLA-A2 restricted CTL epitopes specific of the HIVCON AFP. First,prediction algorithms are used to identify potential peptides that maybind well to HLA-A2 protein (Tourdot et al. (2000) Eur J Immunol30:3411-3421). Second, a library of 15-mer peptides that overlap byeleven amino acids and span the entire length of the HIVCON AFP aredesigned. The library of 15-mer peptides are distributed in a number ofpeptide pools based on sequence overlap that will reduce the number offunctional assays that will be performed. Both the prediction basedpeptides and the 15-mer library peptides are synthesized and purified bystandard proteins synthesis techniques. These peptides are tested fortheir ability to bind to the HHD single chain in an assay that measurespeptide binding by stabilization of cell surface MHC molecules (Carmonet al. (2002) J Clin Invest 110:453-462). Upon identification of apeptide pool that induces the desired CTL response, fractionation of thepeptide pools will identify the individual peptide that induces the CTLresponse.

HHD mice are immunized intramuscularly with pTH.HIVCON in PBS undergeneral anesthesia. Splenocytes for bulk CTL culture are preparedessentially as described in Example 5. The ability of the predictionbased peptides and the library peptides to induce broad CTL response areassessed in a variety of ways, including an ex vivo intracellularcytokine staining assay (essentially as described in Example 6) and anin vitro cytotoxicity assay that measures CTL induces cell lysis oftarget cells (essentially as described in Example 5).

Initially, the immunogeni city of the pTH.HIVCON and MVA.HIVCON vaccinesin BALB/c are confirmed using a C-terminal H-2D^(d)-restricted epitopeRGPGRAFVTI (called H). Using overlapping peptide across the whole HIVCONprotein, the frequencies of immunogenic epitopes are estimated invarious mouse strains. Because the above epitope is stronglyimmunodominant in the H-2^(d) haplotype, experiments in BALB/c mice arecarried out using HIVCONdH vaccines, from which the H epitope wasdeleted (Example 1). Immune splenocytes from HLA-A2 (HHD) and HLA-B27transgenic mice are also tested on target cells matched for theappropriate HLA molecules pulsed with overlapping HIVCON peptides.Alternatively, HIVCON-induced T cells from the HLA-transgenic mice aretested on HLA-matched, phytohemagglutinin (PHA)-blasted, HIV-1-infectedhuman CD4+ cells. Second, the immunogenicity of the DNA-MVA/HIVCON innon-human primates is examined. Third, an important experiment is toassess if HIV-infected individuals have responses that can recognizeHIVCON-derived peptides. This is performed with either fresh or inculture-expanded IFN-gamma ELISPOTs, intracellular cytokine staining orkilling assays where autologous B-LCLs are available. Positive responsesin the HIV-infected individuals would demonstrate that the HIV-infectedcells indeed process and present epitopes from the conserved HIVregions.

Example 11 Immunogenicity in Non-Human Primates

Rhesus macaques (Macaca mulatta) positive for the Mamu-A*01 allele ofMHC class I are immunized with a DNA prime-MVA boost regimen. Threemacaques (monkeys 1-3) will receive immunizations with plasmidspTHr.HIVCON at weeks 0 and 4, followed by immunization with recombinantMVA.HIVCON at weeks 20 and 24. Two macaques (monkeys 4 and 5) willreceive the same priming immunizations but boosted with recombinantMVA.HIVCON at weeks 8 and 12. The immunizations consist of 1 mg of eachplasmid in 0.5 ml of 140 mM NaCl, 0.5 mM Tris-HCl, pH 7.7 and 0.05 mMEDTA delivered i.m. or 5×10⁷ pfu of each MVA in 0.1 ml of 140 mM NaC1and 10 mM Tris-HCl, pH 7.7 delivered intradermally (i.d.). The HIVCONvaccines are delivered into the animals' arms. All immunizations andvenipunctures are carried out under sedation with ketamine and theanimals were regularly clinically examined.

Monkey PBMC are isolated from heparinized blood using the Lymphoprep™cushion centrifugation (Nycomed Pharma AS). PBMCs are cultured for 2weeks with peptides derived from the SIV Gag (CTPDYNQM) proteins forpeptide-specific expansion. Tetrameric MHC/peptide complexes forMamu-A*01/Gag are prepared as described elsewhere. Immunogenicity isassessed using PBMCs restimulated with the Gag peptide for 2 weeks at37° C., 5% CO₂ with an addition of huIL-2 on day 3. On the day of theassay, the cells are reacted with phycoerythrin (PE)-conjugatedMamu-A*01/peptides tetrameric complexes and mouse anti-huCD8-PerCP mAb(BD PharMingen) and analyzed by FACS.

Using both the Mamu-A*01-restricted and overlapping peptides derivedfrom the HIVA and RENTA immunogens, multi-specific responses aredetected to the HIVCON vaccines in an IFN-γ ELISPOT assay ex vivo. TheIFN-γ ELISPOT assay is carried out on DNA primed-MVA boosted animalsusing freshly isolated PBMC (drawn at week 22) for both theMamu-A*01-restricted epitope peptides and overlapping pools of peptidesacross the HIVCON proteins. The procedures and reagents of the MABTECHkit (Mabtech AB) are used. Briefly, PBMC are isolated on a Lymphoprepcushion and incubated at 37° C., 5% CO₂ for 24 hours with the indicatedpeptide or peptide pool. The released IFN-γ is captured by a mAbimmobilized on the bottom of assay wells, visualized by combination of asecond mAb coupled to an enzyme and a chromogenic substrate. Spots arecounted using an ELISPOT reader (Autoimmun Diagnostika GmbH, Germany)and expressed as spot-forming units per 10⁶ splenocytes.

For monkey bulk CTL cultures, 8×10⁶ isolated PBMC are restimulated with10 μm peptide (or peptide pool) in 100 μl of R20 in 5% CO₂ at 37° C. for1 hour and resuspended in total of 4 ml of R20 supplemented with 25ng/ml of huIL-7 in two 24-well-plate wells. On day 3, Lymphocult-T(Biotest AG) is added to the final concentration of 10% (v/v). On day 8,5×10⁶ peptide-pulsed irradiated autologous B lymphoblastoid cell lines(B-LCL) is added to the cultures followed by Lymphocult-T on day 11.Cytolytic tests were carried out on day 14.

For the ⁵¹Cr-release assay, the effector cells are diluted sequentially2-fold in U-bottom wells 96-well plates (Costar) at effector to targetratios of 50:1, 25:1 and 12:1. Five thousand ⁵¹Cr-labelled autologousB-LCL pulsed (2 μg/ml) or unpulsed with peptide (Gag) or peptide pools(for HIVCON) are added to the effectors and incubated at 37° C. for 6hours. Percent specific lysis is calculated as for the mouse lysisassays. Spontaneous release is for all samples below 20% of the totalcounts.

Example 12 Immunogenicity of HIVCON Vaccines in BALB/c Mice

Sec FIG. 11(A) which shows immunogenicities of the individual vaccinecomponents. Splenocytes from individual animals were tested ex vivo forthe production of IFN-γ in an ELISPOT assay using the RGPGRAFVTIepitope. See FIG. 11(B), where experiments were performed as above (datain FIG. 11(B)), but with higher doses for the MVA.HIVCON and Ad.HIVCONvaccines. FIG. 11(C) demonstrates the immunogenicities of individualvaccine components compared to various prime-boost vaccination regimes,using an IFN-γ ELISPOT assay as above. FIG. 11(D) demonstratesimmunogenicities of individual vaccine components compared to a DNAprime-MVA boost vaccination regime. Splenocytes from individual animalswere restimulated for 5 days in culture with the RGPGRAFVTI peptide andtested in a ⁵¹Cr-release assay on peptide pulsed (full) or unpulsed(open) targets.

Example 13 Immunogenicity of the HIVCON and HIVCONΔH Vaccines in BALB/cMice

Splenocytes from individual animals were tested ex vivo for theproduction of IFN-γ in an ELISPOT assay using pools of overlappingpeptides spanning the entire HIVCON sequence. Animals were immunizedwith 100 μg of pTH.HIVCON at 0 weeks, 10⁸ PFU of Ad.HIVCON at 2 weeks,and 10⁷ PFU of MVA.HIVCON at 8 weeks. Animals were sacrificed at 10weeks. The results are illustrated in FIG. 12(A). A similar experimentwas performed but using animals immunized with 100 μg of pTH.HIVCONΔH at0 weeks and 10⁷ PFU of MVA.HIVCONμH at 2 weeks. Animals were sacrificedat 4 weeks. The results are illustrated in FIG. 12(B). The reactivepeptides in pools 1, 3 and 4 were identified.

Example 14 Immunogenicity of the HIVCON Vaccine in HLA-A2 TransgenicMice HHD

Splenocytes from individual HHD animals were tested ex vivo for theproduction of IFN-γ in an ELISPOT assay using pools of overlappingpeptides spanning the entire HIVCON sequence. Animals were immunizedwith 100 μg of pTH.HIVCON at week 0, 10⁸ PFU of Ad.HIVCON at week 2, and10⁷ PFU of MVA.HIVCON at week 8. Animals were sacrificed at week 10. Theresults are demonstrated in FIG. 13. Reactive peptides in pools 3 and 4were identified.

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(2004) “Topical delivery of imiquimod to    a mouse model as a novel adjuvant for human immunodeficiency virus    (HIV) DNA” Vaccine 22(13-14): 1791-8.-   Beattie, T., Kaul, R., Rostron, T., Dong, T., Easterbrook, P.,    Jaoko, W., Kimani, J., Plummer, F., McMichael, A., and    Rowland-Jones, S. (2004) “Screening for HIV-specific T-cell    responses using overlapping 15-mer peptide pools or optimized    epitopes” AIDS 18(11): 1595-8.-   Ito, Y., Grivel, J. C., and Margolis, L. (2003) “Real-time PCR assay    of individual human immunodeficiency virus type 1 variants in    coinfected human lymphoid tissues” J. Clin. Microbiol. 41(5):    2126-31.-   Sun, Y., Iglesias, E., Samri, A., Kamkamidze, G., Decoville, T.,    Carcelain, G., Autran, B. (2003) “A systematic comparison of methods    to measure HIV-1 specific CD8 T cells” J. Immunol. Meth. 272(1-2):    23-34.-   Shacklett, B. L. (2002) “Beyond ⁵¹Cr release: New methods for    assessing HIV-1-specific CD8+ T cell responses in peripheral blood    and mucosal tissues” Clin. Exp. Immunol. 130(2): 172-82.-   Hsiao, C. L. and Carbon, J. (1981) “Direct selection procedure for    the isolation of functional centromeric DNA”. Proc Natl Acad Sci USA    78(6): 3760-4.    The invention is further described by the following numbered    paragraphs:-   1. An artificial fusion protein (AFP) comprising an HIV Gag domain;    one or more HIV Pol domains; an HIV Vif domain; and one or more HIV    Env domains.-   2. The AFP of Paragraph 1, wherein each of the HIV Gag, Pol, Vif,    and Env are selected so that the AFP induces an immune response to a    pre-determined HIV Clade.-   3. The AFP of Paragraph 2, wherein the HIV Clade is selected from    the group consisting of Clade A, A1, A2, B, C and D.-   4. The AFP of Paragraph 1, wherein the amino acid sequences for each    of the HIV Gag, Pol, Vif, and Env domains are from an HTV consensus    sequence for the same HIV Clade.-   5. The AFP of Paragraph 4, wherein the HIV Clade is selected from    the group consisting of Clade A, A1, A2, B, C and D.-   6. The AFP of Paragraph 1, wherein the amino acid sequences for each    of the HIV Gag, Pol, Vif, and Env domains are from HIV consensus    sequences for different HIV Clades.-   7. The AFP of Paragraph 6, wherein the HIV Clade is selected from    the group consisting of Clade A, A1, A2, B, C and D.-   8. The AFP of Paragraph 6, wherein the amino acid sequences for each    of HIV Gag, Pol, Vif, and Env vary by from about 0% to about 10%    between HIV Clades.-   9. The AFP of Paragraph 8, wherein the amino acid sequences for each    of HTV Gag, Pol, Vif, and Env vary by from about 0% to about 8%    between HIV Clades.-   10. The AFP of Paragraph 9, wherein the amino acid sequences for    each of HIV Gag, Pol, Vif, and Env vary by from about 0% to about 6%    between HIV Clades.-   11. The AFP of Paragraph 1, wherein the domains are present from N-    to C-terminus in any order that does not recreate a    naturally-occurring HIV protein.-   12. The AFP of Paragraph 11, wherein the domains are joined with or    without intervening sequences.-   13. The AFP of Paragraph 1, wherein the domains are present from N-    to C-terminus in order of: HIV Gag domain, a first HIV Pol domain,    HIV Vif domain, a second HIV Pol domain, a first HIV Env domain, a    third HIV Pol domain, and a second HIV Env domain.-   14. The AFP of Paragraph 13, wherein the domains are joined with or    without intervening sequences.-   15. The AFP of Paragraph 1, wherein the HIV Gag domain comprises a    sequence of amino acids from an HIV isolate or an HIV consensus    sequence corresponding to amino acids 1-135 of SEQ ID NO: 2.-   16. The AFP of Paragraph 15, wherein the HIV Gag domain comprises    amino acids 1-135 of SEQ ID NO: 2.-   17. The AFP of Paragraph 1, wherein the HIV Gag domain comprises    three HIV Gag subdomains.-   18. The AFP of Paragraph 17, wherein each of the three HIV Gag    subdomains comprise a sequence of amino acids that are from the same    HIV Clade.-   19. The AFP of Paragraph 17, wherein each of the three HIV Gag    subdomains comprise a sequence of amino acids that are from    different HIV Clades.-   20. The AFP of Paragraph 17, wherein the first HTV Gag subdomain    comprises a sequence of amino acids corresponding to amino acids    1-56 of SEQ ID NO: 2 and wherein the sequence is from HIV Clade C.-   21. The AFP of Paragraph 17, wherein the second HIV Gag subdomain    comprises a sequence of amino acids corresponding to amino acids    57-96 of SEQ ID NO: 2 and wherein the sequence is from HIV Clade D.-   22. The AFP of Paragraph 17, wherein the third HIV Gag subdomain    comprises a sequence of amino acids corresponding to amino acids    97-135 of SEQ ID NO: 2 and wherein the sequence is from HIV Clade A.-   23. The AFP of Paragraph 1, which comprises three HIV Pol domains.-   24. The AFP of Paragraph 23, wherein the first HIV Pol domain    comprises a sequence of amino acids from an HIV isolate or an HIV    consensus sequence corresponding to amino acids 136-393 of SEQ ID    NO: 2, wherein the second HIV Pol domain comprises a sequence of    amino acids from an HIV isolate or an HIV consensus sequence    corresponding to amino acids 422-484 of SEQ ID NO: 2, and wherein    the third HIV Pol domain comprises a sequence of amino acids from an    HIV isolate or an HTV consensus sequence corresponding to amino    acids 522-723 of SEQ ID NO: 2.-   25. The AFP of Paragraph 24, wherein the first HIV Pol domain    comprises amino acids 136-393 of SEQ ID NO: 2 and the second HIV Pol    domain comprises amino acids 422-484 of SEQ ID NO: 2 and the third    HIV Pol domain comprises amino acids 522-723 of SEQ ID NO: 2.-   26. The AFP of Paragraph 24, wherein each HIV Pol domain comprises    at least two HIV Pol subdomains.-   27. The AFP of Paragraph 26, wherein each of the at least two HIV    Pol subdomains comprise a sequence of amino acids that are from the    same HIV Clade.-   28. The AFP of Paragraph 26, wherein each of the at least two HIV    Pol subdomains comprise a sequence of amino acids that are from    different HIV Clades.-   29. The AFP of Paragraph 26, wherein the first HIV Pol domain    comprises two HIV Pol subdomains.-   30. The AFP of Paragraph 29, wherein the first HIV Pol subdomain    comprises a sequence of amino acids corresponding to amino acids    136-265 of SEQ ID NO: 2 and wherein the sequence is from HIV Clade    B.-   31. The AFP of Paragraph 29, wherein the second HIV Pol subdomain    comprises a sequence of amino acids corresponding to amino acids    266-393 of SEQ ID NO: 2 and wherein the sequence is from HIV Clade    C.-   32. The AFP of Paragraph 26, wherein the second HIV Pol domain    comprises two HIV Pol subdomains.-   33. The AFP of Paragraph 32, wherein the first HIV Pol subdomain    comprises a sequence of amino acids corresponding to amino acids    432-467 of SEQ ID NO: 2 and wherein the sequence is from HIV Clade    A.-   34. The AFP of Paragraph 32, wherein the second HIV Pol subdomain    comprises a sequence of amino acids corresponding to amino acids    468-494 of SEQ ID NO: 2 and wherein the sequence is from HIV Clade    B.-   35. The AFP of Paragraph 26, wherein the third HIV Pol domain    comprises four HIV Pol subdomains.-   36. The AFP of Paragraph 35, wherein the first HIV Pol subdomain    comprises a sequence of amino acids corresponding to amino acids    522-556 of SEQ ID NO: 2 and wherein the sequence is from HIV Clade    D.-   37. The AFP of Paragraph 35, wherein the second HIV Pol subdomain    comprises a sequence of amino acids corresponding to amino acids    557-629 of SEQ ID NO: 2 and wherein the sequence is from HIV Clade    A.-   38. The AFP of Paragraph 35, wherein the third HIV Pol subdomain    comprises a sequence of amino acids corresponding to amino acids    630-676 of SEQ ID NO: 2 and wherein the sequence is from HIV Clade    B.-   39. The AFP of Paragraph 35, wherein the fourth HIV Pol subdomain    comprises a sequence of amino acids corresponding to amino acids    677-723 of SEQ ID NO: 2 and wherein the sequence is from HIV Clade    C.-   40. The AFP of Paragraph 1, wherein the HIV Vif domain comprises a    sequence of amino acids from an HIV isolate or an HIV consensus    sequence corresponding to amino acids 394-421 of SEQ ID NO: 2.-   41. The AFP of Paragraph 40, wherein the HIV Vif domain comprises    amino acids 394-421 of SEQ ID NO: 2.-   42. The AFP of Paragraph 40, wherein the HIV Vif domain comprises a    sequence from HIV Clade D.-   43. The AFP of Paragraph 1, wherein the first Env domain comprises a    sequence of amino acids from an HIV isolate or an HIV consensus    sequence corresponding to amino acids 485-521 of SEQ ID NO: 2, and    wherein the second HIV Env domain comprises a sequence of amino    acids from an HIV isolate or an HIV consensus sequence corresponding    to amino acids 724-777 of SEQ ID NO: 2.-   44. The AFP of Paragraph 1, wherein the first HIV Env domain    comprises amino acids 485-521 of SEQ ID NO: 2, and wherein the    second HIV Env domain comprises amino acids 724-777 of SEQ ID NO: 2.-   45. The AFP of Paragraph 43, wherein the first Env domain comprises    a sequence from HIV Clade C.-   46. The AFP of Paragraph 43, wherein the second Env domain comprises    a sequence from HIV Clade D.-   47. The AFP of Paragraph 1, comprising amino acids 1-777 of SEQ ID    NO: 2.-   48. The AFP of Paragraph 1, further comprising one or more non-human    CTL domains for monitoring immune responses to the AFP in a    laboratory mammal.-   49. The AFP of Paragraph 48, wherein the one or more non-human CTL    domains is selected from the group consisting of the SIV tat CTL    epitope, the pb9 epitope, the P18-I10 epitope and the SIV Gag p27    epitope.-   50. The AFP of Paragraph 49, wherein the additional domains are the    SIV Gag p27 CTL epitope and the P18-I10 epitope.-   51. The AFP of Paragraph 48, further comprising a marker domain.-   52. The AFP of Paragraph 51, wherein the marker domain encodes an    epitope for a monoclonal antibody selected from the group consisting    of Pk, Flag, HA, myc, GST or His epitopes.-   53. The AFP of Paragraph 52, wherein the marker domain encodes the    Pk epitope.-   54. The AFP of Paragraph 1, comprising amino acids 1-806 of SEQ ID    NO: 2.-   55. An isolated nucleic acid having a nucleotide sequence encoding    the AFP of any one of Paragraphs 1-47.-   56. An isolated nucleic acid having a nucleotide sequence encoding    the AFP of Paragraph 50.-   57. An isolated nucleic acid having a nucleotide sequence encoding    the AFP of Paragraph 53.-   58. An isolated nucleic acid having a nucleotide sequence encoding    the AFP of Paragraph 55.-   59. An isolated nucleic acid, wherein the nucleic acid has a    nucleotide sequence comprising SEQ ID NO: 1.-   60. An expression vector comprising a nucleic acid having a    nucleotide sequence encoding the AFP of any one of Paragraphs 1-47    operably linked to at least one nucleic acid control sequence.-   61. An expression vector comprising a nucleic acid having a    nucleotide sequence encoding the AFP of Paragraph 50 operably linked    to at least one nucleic acid control sequence.-   62. An expression vector comprising a nucleic acid having a    nucleotide sequence encoding the AFP of Paragraph 53 operably linked    to at least one nucleic acid control sequence.-   63. An expression vector comprising a nucleic acid having a    nucleotide sequence encoding the AFP of Paragraph 55 operably linked    to at least one nucleic acid control sequence.-   64. The expression vector of Paragraph 60, wherein the vector is a    plasmid vector, a viral vector, an insect vector, a yeast vector or    a bacterial vector.-   65. The expression vector of Paragraph 64, wherein the plasmid    vector is pTH or pTHr.-   66. The expression vector of Paragraph 64, wherein the viral vector    is an alphavirus replicon vector, an adeno-associated virus vector,    an adenovirus vector, a retrovirus vector or a poxvirus vector.-   67. The expression vector of Paragraph 66, wherein the vector is a    poxvirus vector selected from the group consisting of vaccinia virus    and avipox virus.-   68. The expression vector of Paragraph 66, wherein the poxvirus is    an attenuated poxvirus selected from the group consisting of    modified vaccinia Ankara (MVA), NYVAC, TROVAC, and ALVAC.-   69. The expression vector of Paragraph 64, wherein the bacterial    vector is a live, attenuated Salmonella or a Shigella vector.-   70. The expression vector of Paragraph 60, wherein the nucleic acid    control sequence is a cytomegalovirus (CMV) immediate early    promoter.-   71. The expression vector of any one of Paragraphs 60-68, wherein    the codons encoding the AFP are those of highly expressed genes for    a target subject or host cell in which the AFP is to be expressed.-   72. The expression vector of Paragraph 71, wherein the target    subject or host cell is a human.-   73. The expression vector of Paragraph 65, wherein the expression    vector and nucleic acid together is pTHr.HTVCON.-   74. The expression vector of Paragraph 68, wherein the expression    vector and nucleic acid together is MVA.HIVCON.-   75. A host cell comprising the expression vector of Paragraph 60.-   76. A host cell comprising the expression vector of Paragraph 61.-   77. A host cell comprising the expression vector of Paragraph 62.-   78. A host cell comprising the expression vector of Paragraph 63.-   79. A host cell comprising the expression vector of Paragraph 71.-   80. A host cell comprising the expression vector of Paragraph 72.-   81. A host cell comprising the expression vector of Paragraph 73.-   82. A method of preparing an AFP, which comprises (a) culturing the    host cell of any one of Paragraphs 75-81 for a time and under    conditions to express the AFP; and (b) recovering the AFP.-   83. A method for introducing into and expressing an AFP in an    animal, which comprises delivering an expression vector of Paragraph    60 into the animal and thereby obtaining expression of the AFP in    the animal.-   84. A method for introducing into and expressing an AFP in an    animal, which comprises delivering an expression vector of Paragraph    61 into the animal and thereby obtaining expression of the AFP in    the animal.-   85. A method for introducing into and expressing an AFP in an    animal, which comprises delivering an expression vector of Paragraph    62 into the animal and thereby obtaining expression of the AFP in    the animal.-   86. A method for introducing into and expressing an AFP in an    animal, which comprises delivering an expression vector of any one    of Paragraphs 63-70, 73, or 74 into the animal and thereby obtaining    expression of the AFP in the animal.-   87. A method for expressing an AFP in animal cells, which    comprises (a) introducing an expression vector of Paragraph 60 into    the animal cells; and (b) culturing those cells under conditions    sufficient to express the AFP.-   88. A method for expressing an AFP in animal cells, which    comprises (a) introducing an expression vector of Paragraph 61 into    the animal cells; and (b) culturing those cells under conditions    sufficient to express the AFP.-   89. A method for expressing an AFP in animal cells, which    comprises (a) introducing an expression vector of Paragraph 62 into    the animal cells; and (b) culturing those cells under conditions    sufficient to express the AFP.-   90. A method for expressing an AFP in animal cells, which    comprises (a) introducing an expression vector of Paragraph 63-70,    73 or 74 into the animal cells; and (b) culturing those cells under    conditions sufficient to express the AFP.-   91. A method for inducing an immune response in an animal, which    comprises delivering an expression vector of Paragraph 60 into the    animal, wherein the AFP is expressed at a level sufficient to induce    an immune response to the AFP.-   92. A method for inducing an immune response in an animal, which    comprises delivering an expression vector of Paragraph 61 into the    animal, wherein the AFP is expressed at a level sufficient to induce    an immune response to the AFP.-   93. A method for inducing an immune response in an animal, which    comprises delivering an expression vector of Paragraph 62 into the    animal, wherein the AFP is expressed at a level sufficient to induce    an immune response to the AFP.-   94. A method for inducing an immune response in an animal, which    comprises delivering an expression vector of any one of Paragraphs    63-70, 73 or 74 into the animal, wherein the AFP is expressed at a    level sufficient to induce an immune response to the AFP.-   95. A method for inducing an immune response in an animal, which    comprises delivering an AFP of any one of Paragraphs 1-47 into the    animal in an amount sufficient to induce an immune response to the    AFP.-   96. A method for inducing an immune response in an animal, which    comprises delivering an AFP of Paragraph 48 into the animal in an    amount sufficient to induce an immune response to the AFP.-   97. A method for inducing an immune response in an animal, which    comprises delivering an AFP of Paragraph 51 into the animal in an    amount sufficient to induce an immune response to the AFP.-   98. A method for inducing an immune response in an animal, which    comprises delivering an AFP of Paragraph 54 into the animal in an    amount sufficient to induce an immune response to the AFP.-   99. A method of inducing an immune response against HIV in a human    subject, which comprises administering an immunogen one or more    times to a subject, wherein the immunogen is selected from the group    consisting of (i) an AFP of any one of Paragraphs 1-47 or 54, (ii) a    nucleic acid encoding the AFP, and (iii) an expression vector    encoding the AFP; and wherein the AFP is administered in an amount    or expressed at a level sufficient to induce an HIV-specific CTL    immune response in the subject.-   100. The method of Paragraph 99, wherein the subject receives at    least two administrations of the immunogen at intervals of at least    two weeks or at least four weeks.-   101. The method of Paragraph 100, wherein another HIV immunogen is    administered at the same time or at different times as part of an    overall immunization regime.-   102. A method of inducing an immune response against HIV in a human    subject, which comprises administering to the subject at least one    priming dose of an HIV immunogen and at least one boosting dose of    an HIV immunogen, wherein the immunogen in each dose can be the same    or different, provided that at least one of the immunogens is an AFP    of any one of Paragraphs 1-47 or 54 or is a nucleic acid or an    expression vector encoding the AFP, wherein the immunogens are    administered in an amount or expressed at a level sufficient to    induce an HIV-specific T-cell immune response in the subject.-   103. The method of Paragraph 102, wherein the interval between each    dose is at least two weeks or at least four weeks.-   104. The method of Paragraph 102, wherein pTHr.HIVCON is    administered one or more times as a priming dose.-   105. The method of Paragraph 102, wherein MVA.HIVCON is administered    one or more times as a boosting dose.-   106. The method of Paragraph 104, wherein MVA.HIVCON is administered    one or more times as a boosting dose.-   107. The method of Paragraph 102, which comprises administering two    priming doses and administering two boosting doses, wherein the    immunogen used for the priming doses is a plasmid vector and the    immunogen used for the boosting doses is a viral vector.-   108. The method of Paragraph 104, wherein the viral vector is an MVA    vector.-   109. The method of Paragraph 107, wherein each of the priming doses    is a mixture of vectors selected from the group consisting of    pTHr.HIVA, pTHr.RENTA, and pTHr.HIVCON and each of the boosting    doses is a mixture of vectors selected from the group consisting of    MVA.RENTA, MVA.HIVA, and MVA.HIVCON.-   110. An immunogenic composition comprising an AFP of any one of    Paragraphs 1-47 or 54, or a nucleic acid encoding the AFP, or an    expression vector encoding the AFP; and a pharmaceutically    acceptable carrier.-   111. An immunogenic composition comprising an AFP of Paragraph 48,    or a nucleic acid encoding the AFP, or an expression vector encoding    the AFP; and a pharmaceutically acceptable carrier.-   112. An immunogenic composition comprising an AFP of Paragraph 51,    or a nucleic acid encoding the AFP, or an expression vector encoding    the AFP; and a pharmaceutically acceptable carrier.-   113. An immunogenic composition comprising an expression vector of    any one of Paragraphs 63-70, 73 or 74; and a pharmaceutically    acceptable carrier.-   114. The composition of Paragraph 110, which further comprises an    adjuvant.-   115. The composition of Paragraph 111, which further comprises an    adjuvant.-   116. The composition of Paragraph 112, which further comprises an    adjuvant.-   117. The composition of Paragraph 113, which further comprises an    adjuvant.-   118. The composition of any of Paragraphs 114-117, wherein the    adjuvant is selected from the group consisting of mineral salts,    polynucleotides, polyarginines, ISCOMs, saponins, monophosphoryl    lipid A, imiquimod, CCR-5 inhibitors, toxins, polyphosphazenes,    cytokines, immunoregulatory proteins, immunostimulatory fusion    proteins, co-stimulatory molecules, and combinations thereof.-   119. A library of immunogenic polypeptides, comprising a plurality    of polypeptides comprising at least 15 successive amino acids of SEQ    ID NO: 2, wherein each immunogenic polypeptide corresponds to at    least a portion or a fragment of SEQ ID NO: 2.-   120. The library of Paragraph 119, wherein the plurality of    immunogenic polypeptides correspond in total to the entire length of    SEQ ID NO: 2.-   121. The library of Paragraph 119, wherein each polypeptide    comprises overlapping amino acid sequences.-   122. The library of Paragraph 121, wherein the sequences overlap by    at least eleven amino acids.-   123. A method of identifying a CTL epitope against HIV from the    library of Paragraph 119 in a cell expressing MHC Class I protein,    comprising the steps of:-   a. Contacting the cell with the library of Paragraph 119;-   b. Selectively binding the library with the MHC protein of the cell;-   c. Isolating a polypeptide of the library that selectively binds to    MHC, and;-   d. Sequencing the polypeptide, thereby identifying the CTL epitope.-   124. The method of Paragraph 123, wherein the cell is an    antigen-presenting cell.-   125. The method of Paragraph 124, wherein the cell is a splenocyte.-   126. The method of Paragraph 123, wherein the cell is a human cell.-   127. The method of Paragraph 126, wherein the MHC Class I protein is    human leukocyte antigen (HLA).-   128. The method of Paragraph 123, wherein selective binding is    measured by flow cytometry.-   129. The method of Paragraph 123, wherein the polypeptide is    isolated by chromatography.

Having thus described in detail preferred embodiments of the presentinvention, it is to be understood that the invention defined by theabove paragraphs is not to be limited to particular details set forth inthe above description as many apparent variations thereof are possiblewithout departing from the spirit or scope of the present invention.

What is claimed is:
 1. A library of immunogenic polypeptides, whereinthe library comprises a plurality of polypeptides and wherein eachpolypeptide comprises at least 8-15 successive amino acids of SEQ ID NO:2 or SEQ ID NO:
 4. 2. The library of claim 1, wherein the plurality ofimmunogenic polypeptides correspond in total to the entire length of SEQID NO: 2 or SEQ ID NO:
 4. 3. The library of claim 1, wherein the 8-15successive amino acids comprises overlapping amino acid sequences. 4.The library of claim 3, wherein the overlapping amino acids are at leasteleven amino acids.
 5. The library of claim 1, wherein the polypeptidesare synthesized polypeptides.
 6. The library of claim 1, which furthercomprises an adjuvant.
 7. The library of claim 6, wherein the adjuvantis selected from the group consisting of mineral salts, polynucleotides,polyarginines, ISCOMs, saponins, monophosphoryl lipid A, imiquimod,CCR-5 inhibitors, toxins, polyphosphazenes, cytokines, immunoregulatoryproteins, immunostimulatory fusion proteins, co-stimulatory molecules,and combinations thereof.
 8. The library of claim 1, wherein the eachpolypeptide is 15 amino acids long.